WorldWideScience

Sample records for brain atlas concordance

  1. Baby brain atlases.

    Science.gov (United States)

    Oishi, Kenichi; Chang, Linda; Huang, Hao

    2018-04-03

    The baby brain is constantly changing due to its active neurodevelopment, and research into the baby brain is one of the frontiers in neuroscience. To help guide neuroscientists and clinicians in their investigation of this frontier, maps of the baby brain, which contain a priori knowledge about neurodevelopment and anatomy, are essential. "Brain atlas" in this review refers to a 3D-brain image with a set of reference labels, such as a parcellation map, as the anatomical reference that guides the mapping of the brain. Recent advancements in scanners, sequences, and motion control methodologies enable the creation of various types of high-resolution baby brain atlases. What is becoming clear is that one atlas is not sufficient to characterize the existing knowledge about the anatomical variations, disease-related anatomical alterations, and the variations in time-dependent changes. In this review, the types and roles of the human baby brain MRI atlases that are currently available are described and discussed, and future directions in the field of developmental neuroscience and its clinical applications are proposed. The potential use of disease-based atlases to characterize clinically relevant information, such as clinical labels, in addition to conventional anatomical labels, is also discussed. Copyright © 2018. Published by Elsevier Inc.

  2. Multiple brain atlas database and atlas-based neuroimaging system.

    Science.gov (United States)

    Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

    1997-01-01

    For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

  3. Computational and mathematical methods in brain atlasing.

    Science.gov (United States)

    Nowinski, Wieslaw L

    2017-12-01

    Brain atlases have a wide range of use from education to research to clinical applications. Mathematical methods as well as computational methods and tools play a major role in the process of brain atlas building and developing atlas-based applications. Computational methods and tools cover three areas: dedicated editors for brain model creation, brain navigators supporting multiple platforms, and atlas-assisted specific applications. Mathematical methods in atlas building and developing atlas-aided applications deal with problems in image segmentation, geometric body modelling, physical modelling, atlas-to-scan registration, visualisation, interaction and virtual reality. Here I overview computational and mathematical methods in atlas building and developing atlas-assisted applications, and share my contribution to and experience in this field.

  4. Mindboggle: Automated brain labeling with multiple atlases

    International Nuclear Information System (INIS)

    Klein, Arno; Mensh, Brett; Ghosh, Satrajit; Tourville, Jason; Hirsch, Joy

    2005-01-01

    To make inferences about brain structures or activity across multiple individuals, one first needs to determine the structural correspondences across their image data. We have recently developed Mindboggle as a fully automated, feature-matching approach to assign anatomical labels to cortical structures and activity in human brain MRI data. Label assignment is based on structural correspondences between labeled atlases and unlabeled image data, where an atlas consists of a set of labels manually assigned to a single brain image. In the present work, we study the influence of using variable numbers of individual atlases to nonlinearly label human brain image data. Each brain image voxel of each of 20 human subjects is assigned a label by each of the remaining 19 atlases using Mindboggle. The most common label is selected and is given a confidence rating based on the number of atlases that assigned that label. The automatically assigned labels for each subject brain are compared with the manual labels for that subject (its atlas). Unlike recent approaches that transform subject data to a labeled, probabilistic atlas space (constructed from a database of atlases), Mindboggle labels a subject by each atlas in a database independently. When Mindboggle labels a human subject's brain image with at least four atlases, the resulting label agreement with coregistered manual labels is significantly higher than when only a single atlas is used. Different numbers of atlases provide significantly higher label agreements for individual brain regions. Increasing the number of reference brains used to automatically label a human subject brain improves labeling accuracy with respect to manually assigned labels. Mindboggle software can provide confidence measures for labels based on probabilistic assignment of labels and could be applied to large databases of brain images

  5. Brain transcriptome atlases : A computational perspective

    NARCIS (Netherlands)

    Mahfouz, A.M.E.T.A.; Huisman, S.M.H.; Lelieveldt, B.P.F.; Reinders, M.J.T.

    2017-01-01

    The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases

  6. Digital atlas of fetal brain MRI

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, Teresa; Weinberger, E. [Department of Radiology, Seattle Children' s Hospital, Seattle, WA (United States); Matesan, Manuela [University of Washington, Department of Radiology, Seattle, WA (United States); Bulas, Dorothy I. [Division of Diagnostic Imaging and Radiology, Children' s National Medical Center, Washington, DC (United States)

    2010-02-15

    Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download. Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development. (orig.)

  7. Digital atlas of fetal brain MRI

    International Nuclear Information System (INIS)

    Chapman, Teresa; Weinberger, E.; Matesan, Manuela; Bulas, Dorothy I.

    2010-01-01

    Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download. Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development. (orig.)

  8. Digital atlas of fetal brain MRI.

    Science.gov (United States)

    Chapman, Teresa; Matesan, Manuela; Weinberger, Ed; Bulas, Dorothy I

    2010-02-01

    Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C#, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download from http://radiology.seattlechildrens.org/teaching/fetal_brain . Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development.

  9. STUDY ABOUT CLINICAL APPLICATION OF BRAIN ATLAS IN PAEDIATRICS

    Institute of Scientific and Technical Information of China (English)

    MENG Fanhang; LIU Cuiping; RENG Xiaoping; JIANG Lian

    2002-01-01

    Objectives To explore clinical application on brain atlas in paediatrics. Methode: Brain atlas was applied in diagnosis and treatment of paediatric diseases and its clinical value was discussed in 1990 ~2001. The manifestation of these diseases in brain atlas were analysed and the manifestation of CT of 67 cases and manifestations of EEG of 37 cases with that of BA were compared. Results The changes of cerebral electrical activity of these diseases were reflected objectively and showed directly in BA. Conclusion Brain atlas not only can point out quality of disease but also define position of disease. Therefore, brain atlas has important clinical value in paediatrics.

  10. The Cerefy registered clinical brain atlas on CD-ROM. Based on the classic Talairach-Tournoux and Schaltenbrand-Wahren brain atlases. 2. ed.

    International Nuclear Information System (INIS)

    Nowinski, W.L.; Thirunavuukarasuu, A.

    2001-01-01

    This remarkable CD-ROM provides enhanced and extended versions of three world-famous Thieme atlases, (Schaltenbrand and Wahren's Atlas for Stereotaxy of the Human Brain, Talairach and Tournoux's Co-Planar Stereotaxis Atlas of the Human Brain and Referentially Oriented Cerebral MRI Anatomy). It contains the electronic atlases as well as an easy navigation system to facilitate searching for and displaying more than 525 anatomical structures. Revolutionizing the field of brain anatomy, the authors have segmented, labeled, and cross referenced all the information contained in the books, and created contours for all three atlases. The Cerefy registered Clinical Brain Atlas now allows you to electronically navigate these atlases simultaneously on axial, coronal, and sagittal planes, and enjoy the ability to: 1. Access 210 high-quality, fully segmented, and labeled atlas images with corresponding contours, 2. Display and manipulate spatially co-registered atlases, 3. Dynamically label images with structure names and descriptions, and then highlight selected structures in the atlas image, 4. Image zoom in five different levels, mensurate, search, set triplanar, get coordinates, save, and print, 5. Access on-line help, glossary, and supportive atlas materials. (orig.)

  11. Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.

    Science.gov (United States)

    Kuan, Leonard; Li, Yang; Lau, Chris; Feng, David; Bernard, Amy; Sunkin, Susan M; Zeng, Hongkui; Dang, Chinh; Hawrylycz, Michael; Ng, Lydia

    2015-02-01

    The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. A digital atlas of the dog brain.

    Directory of Open Access Journals (Sweden)

    Ritobrato Datta

    Full Text Available There is a long history and a growing interest in the canine as a subject of study in neuroscience research and in translational neurology. In the last few years, anatomical and functional magnetic resonance imaging (MRI studies of awake and anesthetized dogs have been reported. Such efforts can be enhanced by a population atlas of canine brain anatomy to implement group analyses. Here we present a canine brain atlas derived as the diffeomorphic average of a population of fifteen mesaticephalic dogs. The atlas includes: 1 A brain template derived from in-vivo, T1-weighted imaging at 1 mm isotropic resolution at 3 Tesla (with and without the soft tissues of the head; 2 A co-registered, high-resolution (0.33 mm isotropic template created from imaging of ex-vivo brains at 7 Tesla; 3 A surface representation of the gray matter/white matter boundary of the high-resolution atlas (including labeling of gyral and sulcal features. The properties of the atlas are considered in relation to historical nomenclature and the evolutionary taxonomy of the Canini tribe. The atlas is available for download (https://cfn.upenn.edu/aguirre/wiki/public:data_plosone_2012_datta.

  13. Data integration through brain atlasing: Human Brain Project tools and strategies.

    Science.gov (United States)

    Bjerke, Ingvild E; Øvsthus, Martin; Papp, Eszter A; Yates, Sharon C; Silvestri, Ludovico; Fiorilli, Julien; Pennartz, Cyriel M A; Pavone, Francesco S; Puchades, Maja A; Leergaard, Trygve B; Bjaalie, Jan G

    2018-04-01

    The Human Brain Project (HBP), an EU Flagship Initiative, is currently building an infrastructure that will allow integration of large amounts of heterogeneous neuroscience data. The ultimate goal of the project is to develop a unified multi-level understanding of the brain and its diseases, and beyond this to emulate the computational capabilities of the brain. Reference atlases of the brain are one of the key components in this infrastructure. Based on a new generation of three-dimensional (3D) reference atlases, new solutions for analyzing and integrating brain data are being developed. HBP will build services for spatial query and analysis of brain data comparable to current online services for geospatial data. The services will provide interactive access to a wide range of data types that have information about anatomical location tied to them. The 3D volumetric nature of the brain, however, introduces a new level of complexity that requires a range of tools for making use of and interacting with the atlases. With such new tools, neuroscience research groups will be able to connect their data to atlas space, share their data through online data systems, and search and find other relevant data through the same systems. This new approach partly replaces earlier attempts to organize research data based only on a set of semantic terminologies describing the brain and its subdivisions. Copyright © 2018 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  14. Intensity and sulci landmark combined brain atlas construction for Chinese pediatric population.

    Science.gov (United States)

    Luo, Yishan; Shi, Lin; Weng, Jian; He, Hongjian; Chu, Winnie C W; Chen, Feiyan; Wang, Defeng

    2014-08-01

    Constructing an atlas from a population of brain images is of vital importance to medical image analysis. Especially in neuroscience study, creating a brain atlas is useful for intra- and inter-population comparison. Research on brain atlas construction has attracted great attention in recent years, but the research on pediatric population is still limited, mainly due to the limited availability and the relatively low quality of pediatric magnetic resonance brain images. This article is targeted at creating a high quality representative brain atlas for Chinese pediatric population. To achieve this goal, we have designed a set of preprocessing procedures to improve the image quality and developed an intensity and sulci landmark combined groupwise registration method to align the population of images for atlas construction. As demonstrated in experiments, the newly constructed atlas can better represent the size and shape of brains of Chinese pediatric population, and show better performance in Chinese pediatric brain image analysis compared with other standard atlases. Copyright © 2014 Wiley Periodicals, Inc.

  15. Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

    Directory of Open Access Journals (Sweden)

    Kishan Andre Liyanage

    Full Text Available Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap to 1 (complete overlap. For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

  16. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.

    Science.gov (United States)

    Zaslavsky, Ilya; Baldock, Richard A; Boline, Jyl

    2014-01-01

    Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.

  17. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

    Directory of Open Access Journals (Sweden)

    Ilya eZaslavsky

    2014-09-01

    Full Text Available Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today’s data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI. A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS, a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML: XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POIs, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas

  18. A review of structural and functional brain networks: small world and atlas.

    Science.gov (United States)

    Yao, Zhijun; Hu, Bin; Xie, Yuanwei; Moore, Philip; Zheng, Jiaxiang

    2015-03-01

    Brain networks can be divided into two categories: structural and functional networks. Many studies of neuroscience have reported that the complex brain networks are characterized by small-world or scale-free properties. The identification of nodes is the key factor in studying the properties of networks on the macro-, micro- or mesoscale in both structural and functional networks. In the study of brain networks, nodes are always determined by atlases. Therefore, the selection of atlases is critical, and appropriate atlases are helpful to combine the analyses of structural and functional networks. Currently, some problems still exist in the establishment or usage of atlases, which are often caused by the segmentation or the parcellation of the brain. We suggest that quantification of brain networks might be affected by the selection of atlases to a large extent. In the process of building atlases, the influences of single subjects and groups should be balanced. In this article, we focused on the effects of atlases on the analysis of brain networks and the improved divisions based on the tractography or connectivity in the parcellation of atlases.

  19. Digital gene atlas of neonate common marmoset brain.

    Science.gov (United States)

    Shimogori, Tomomi; Abe, Ayumi; Go, Yasuhiro; Hashikawa, Tsutomu; Kishi, Noriyuki; Kikuchi, Satomi S; Kita, Yoshiaki; Niimi, Kimie; Nishibe, Hirozumi; Okuno, Misako; Saga, Kanako; Sakurai, Miyano; Sato, Masae; Serizawa, Tsuna; Suzuki, Sachie; Takahashi, Eiki; Tanaka, Mami; Tatsumoto, Shoji; Toki, Mitsuhiro; U, Mami; Wang, Yan; Windak, Karl J; Yamagishi, Haruhiko; Yamashita, Keiko; Yoda, Tomoko; Yoshida, Aya C; Yoshida, Chihiro; Yoshimoto, Takuro; Okano, Hideyuki

    2018-03-01

    Interest in the common marmoset (Callithrix jacchus) as a primate model animal has grown recently, in part due to the successful demonstration of transgenic marmosets. However, there is some debate as to the suitability of marmosets, compared to more widely used animal models, such as the macaque monkey and mouse. Especially, the usage of marmoset for animal models of human cognition and mental disorders, is still yet to be fully explored. To examine the prospects of the marmoset model for neuroscience research, the Marmoset Gene Atlas (https://gene-atlas.bminds.brain.riken.jp/) provides a whole brain gene expression atlas in the common marmoset. We employ in situ hybridization (ISH) to systematically analyze gene expression in neonate marmoset brains, which allows us to compare expression with other model animals such as mouse. We anticipate that these data will provide sufficient information to develop tools that enable us to reveal marmoset brain structure, function, cellular and molecular organization for primate brain research. Copyright © 2017 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

  20. Toward the holistic, reference, and extendable atlas of the human brain, head, and neck.

    Science.gov (United States)

    Nowinski, Wieslaw L

    2015-06-01

    Despite numerous efforts, a fairly complete (holistic) anatomical model of the whole, normal, adult human brain, which is required as the reference in brain studies and clinical applications, has not yet been constructed. Our ultimate objective is to build this kind of atlas from advanced in vivo imaging. This work presents the taxonomy of our currently developed brain atlases and addresses the design, content, functionality, and current results in the holistic atlas development as well as atlas usefulness and future directions. We have developed to date 35 commercial brain atlases (along with numerous research prototypes), licensed to 63 companies and institutions, and made available to medical societies, organizations, medical schools, and individuals. These atlases have been applied in education, research, and clinical applications. Hundreds of thousands of patients have been treated by using our atlases. Based on this experience, the first version of the holistic and reference atlas of the brain, head, and neck has been developed and made available. The atlas has been created from multispectral 3 and 7 Tesla and high-resolution CT in vivo scans. It is fully 3D, scalable, interactive, and highly detailed with about 3,000 labeled components. This atlas forms a foundation for the development of a multi-level molecular, cellular, anatomical, physiological, and behavioral brain atlas platform.

  1. A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain

    Directory of Open Access Journals (Sweden)

    Ignacio Arganda-Carreras

    2018-03-01

    Full Text Available Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila, one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms. Here, we objectively evaluated the performance of different strategies for building adult Drosophila brain templates and atlases. In addition, we used state-of-the-art registration algorithms to generate a new group-wise inter-sex atlas. Our results highlight the benefit of statistical atlases over individual ones and show that the newly proposed inter-sex atlas outperformed existing solutions for automated registration and annotation of expression patterns. Over 3,000 images from the Janelia Farm FlyLight collection were registered using the proposed strategy. These registered expression patterns can be searched and compared with a new version of the BrainBaseWeb system and BrainGazer software. We illustrate the validity of our methodology and brain atlas with registration-based predictions of expression patterns in a subset of clock neurons. The described registration framework should benefit to brain studies in Drosophila and other insect species.

  2. A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain.

    Science.gov (United States)

    Arganda-Carreras, Ignacio; Manoliu, Tudor; Mazuras, Nicolas; Schulze, Florian; Iglesias, Juan E; Bühler, Katja; Jenett, Arnim; Rouyer, François; Andrey, Philippe

    2018-01-01

    Imaging the expression patterns of reporter constructs is a powerful tool to dissect the neuronal circuits of perception and behavior in the adult brain of Drosophila , one of the major models for studying brain functions. To date, several Drosophila brain templates and digital atlases have been built to automatically analyze and compare collections of expression pattern images. However, there has been no systematic comparison of performances between alternative atlasing strategies and registration algorithms. Here, we objectively evaluated the performance of different strategies for building adult Drosophila brain templates and atlases. In addition, we used state-of-the-art registration algorithms to generate a new group-wise inter-sex atlas. Our results highlight the benefit of statistical atlases over individual ones and show that the newly proposed inter-sex atlas outperformed existing solutions for automated registration and annotation of expression patterns. Over 3,000 images from the Janelia Farm FlyLight collection were registered using the proposed strategy. These registered expression patterns can be searched and compared with a new version of the BrainBaseWeb system and BrainGazer software. We illustrate the validity of our methodology and brain atlas with registration-based predictions of expression patterns in a subset of clock neurons. The described registration framework should benefit to brain studies in Drosophila and other insect species.

  3. Automatic labeling of MR brain images through extensible learning and atlas forests.

    Science.gov (United States)

    Xu, Lijun; Liu, Hong; Song, Enmin; Yan, Meng; Jin, Renchao; Hung, Chih-Cheng

    2017-12-01

    Multiatlas-based method is extensively used in MR brain images segmentation because of its simplicity and robustness. This method provides excellent accuracy although it is time consuming and limited in terms of obtaining information about new atlases. In this study, an automatic labeling of MR brain images through extensible learning and atlas forest is presented to address these limitations. We propose an extensible learning model which allows the multiatlas-based framework capable of managing the datasets with numerous atlases or dynamic atlas datasets and simultaneously ensure the accuracy of automatic labeling. Two new strategies are used to reduce the time and space complexity and improve the efficiency of the automatic labeling of brain MR images. First, atlases are encoded to atlas forests through random forest technology to reduce the time consumed for cross-registration between atlases and target image, and a scatter spatial vector is designed to eliminate errors caused by inaccurate registration. Second, an atlas selection method based on the extensible learning model is used to select atlases for target image without traversing the entire dataset and then obtain the accurate labeling. The labeling results of the proposed method were evaluated in three public datasets, namely, IBSR, LONI LPBA40, and ADNI. With the proposed method, the dice coefficient metric values on the three datasets were 84.17 ± 4.61%, 83.25 ± 4.29%, and 81.88 ± 4.53% which were 5% higher than those of the conventional method, respectively. The efficiency of the extensible learning model was evaluated by state-of-the-art methods for labeling of MR brain images. Experimental results showed that the proposed method could achieve accurate labeling for MR brain images without traversing the entire datasets. In the proposed multiatlas-based method, extensible learning and atlas forests were applied to control the automatic labeling of brain anatomies on large atlas datasets or dynamic

  4. Template based rodent brain extraction and atlas mapping.

    Science.gov (United States)

    Weimin Huang; Jiaqi Zhang; Zhiping Lin; Su Huang; Yuping Duan; Zhongkang Lu

    2016-08-01

    Accurate rodent brain extraction is the basic step for many translational studies using MR imaging. This paper presents a template based approach with multi-expert refinement to automatic rodent brain extraction. We first build the brain appearance model based on the learning exemplars. Together with the template matching, we encode the rodent brain position into the search space to reliably locate the rodent brain and estimate the rough segmentation. With the initial mask, a level-set segmentation and a mask-based template learning are implemented further to the brain region. The multi-expert fusion is used to generate a new mask. We finally combine the region growing based on the histogram distribution learning to delineate the final brain mask. A high-resolution rodent atlas is used to illustrate that the segmented low resolution anatomic image can be well mapped to the atlas. Tested on a public data set, all brains are located reliably and we achieve the mean Jaccard similarity score at 94.99% for brain segmentation, which is a statistically significant improvement compared to two other rodent brain extraction methods.

  5. 3D atlas of brain connections and functional circuits

    Science.gov (United States)

    Pan, Jinghong; Nowinski, Wieslaw L.; Fock, Loe K.; Dow, Douglas E.; Chuan, Teh H.

    1997-05-01

    This work aims at the construction of an extendable brain atlas system which contains: (i) 3D models of cortical and subcortical structures along with their connections; (ii) visualization and exploration tools; and (iii) structures and connections editors. A 3D version of the Talairach- Tournoux brain atlas along with 3D Brodmann's areas are developed, co-registered, and placed in the Talairach stereotactic space. The initial built-in connections are thalamocortical ones. The structures and connections editors are provided to allow the user to add and modify cerebral structures and connections. Visualization and explorations tools are developed with four ways of exploring the brain connections model: composition, interrogation, navigation and diagnostic queries. The atlas is designed as an open system which can be extended independently in other centers according to their needs and discoveries.

  6. A High-Resolution In Vivo Atlas of the Human Brain's Serotonin System.

    Science.gov (United States)

    Beliveau, Vincent; Ganz, Melanie; Feng, Ling; Ozenne, Brice; Højgaard, Liselotte; Fisher, Patrick M; Svarer, Claus; Greve, Douglas N; Knudsen, Gitte M

    2017-01-04

    The serotonin (5-hydroxytryptamine, 5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. Here, we present a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT 1A , 5-HT 1B , 5-HT 2A , and 5-HT 4 ) and the 5-HT transporter (5-HTT). The atlas is created from molecular and structural high-resolution neuroimaging data consisting of positron emission tomography (PET) and magnetic resonance imaging (MRI) scans acquired in a total of 210 healthy individuals. Comparison of the regional PET binding measures with postmortem human brain autoradiography outcomes showed a high correlation for the five 5-HT targets and this enabled us to transform the atlas to represent protein densities (in picomoles per milliliter). We also assessed the regional association between protein concentration and mRNA expression in the human brain by comparing the 5-HT density across the atlas with data from the Allen Human Brain atlas and identified receptor- and transporter-specific associations that show the regional relation between the two measures. Together, these data provide unparalleled insight into the serotonin system of the human brain. We present a high-resolution positron emission tomography (PET)- and magnetic resonance imaging-based human brain atlas of important serotonin receptors and the transporter. The regional PET-derived binding measures correlate strongly with the corresponding autoradiography protein levels. The strong correlation enables the transformation of the PET-derived human brain atlas into a protein density map of the serotonin (5-hydroxytryptamine, 5-HT) system. Next, we compared the regional receptor/transporter protein densities with mRNA levels and uncovered unique associations between protein expression and density at high detail. This new in vivo neuroimaging atlas of the 5-HT system not only provides insight in the human brain's regional protein

  7. A High-Resolution In Vivo Atlas of the Human Brain's Serotonin System

    DEFF Research Database (Denmark)

    Beliveau, Vincent; Ganz-Benjaminsen, Melanie; Feng, Ling

    2017-01-01

    The serotonin (5-hydroxytryptamine, 5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. Here, we present a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4...... with postmortem human brain autoradiography outcomes showed a high correlation for the five 5-HT targets and this enabled us to transform the atlas to represent protein densities (in picomoles per milliliter). We also assessed the regional association between protein concentration and mRNA expression in the human...... brain by comparing the 5-HT density across the atlas with data from the Allen Human Brain atlas and identified receptor- and transporter-specific associations that show the regional relation between the two measures. Together, these data provide unparalleled insight into the serotonin system...

  8. An atlas of the prenatal mouse brain: gestational day 14.

    Science.gov (United States)

    Schambra, U B; Silver, J; Lauder, J M

    1991-11-01

    A prenatal atlas of the mouse brain is presently unavailable and is needed for studies of normal and abnormal development, using techniques including immunocytochemistry and in situ hybridization. This atlas will be especially useful for researchers studying transgenic and mutant mice. This collection of photomicrographs and corresponding drawings of Gestational Day (GD) 14 mouse brain sections is an excerpt from a larger atlas encompassing GD 12-18. In composing this atlas, available published studies on the developing rodent brain were consulted to aid in the detailed labeling of embryonic brain structures. C57Bl/6J mice were mated for 1 h, and the presence of a copulation plug was designated as GD 0. GD 14 embryos were perfused transcardially with 4% paraformaldehyde in 0.1 M phosphate buffer and embedded in paraffin. Serial sections (10 microns thickness) were cut through whole heads in sagittal and horizontal planes. They were stained with hematoxylin and eosin and photographed. Magnifications were 43X and 31X for the horizontal and sagittal sections, respectively. Photographs were traced and line drawings prepared using an Adobe Illustrator on a Macintosh computer.

  9. Digital atlas of the zebra finch (Taeniopygia guttata) brain: a high-resolution photo atlas.

    Science.gov (United States)

    Karten, Harvey J; Brzozowska-Prechtl, Agnieszka; Lovell, Peter V; Tang, Daniel D; Mello, Claudio V; Wang, Haibin; Mitra, Partha P

    2013-11-01

    We describe a set of new comprehensive, high-quality, high-resolution digital images of histological sections from the brain of male zebra finches (Taeniopygia guttata) and make them publicly available through an interactive website (http://zebrafinch.brainarchitecture.org/). These images provide a basis for the production of a dimensionally accurate and detailed digital nonstereotaxic atlas. Nissl- and myelin-stained brain sections are provided in the transverse, sagittal, and horizontal planes, with the transverse plane approximating the more traditional Frankfurt plane. In addition, a separate set of brain sections in this same plane is stained for tyrosine hydroxylase, revealing the distribution of catecholaminergic neurons (dopaminergic, noradrenergic, and adrenergic) in the songbird brain. For a subset of sagittal sections we also prepared a corresponding set of drawings, defining and annotating various nuclei, fields, and fiber tracts that are visible under Nissl and myelin staining. This atlas of the zebra finch brain is expected to become an important tool for birdsong research and comparative studies of brain organization and evolution. Copyright © 2013 Wiley Periodicals, Inc.

  10. Transformations and algorithms in a computerized brain atlas

    International Nuclear Information System (INIS)

    Thurfjell, L.; Bohm, C.; Eriksson, L.; Karolinska Institute/Hospital, Stockholm

    1993-01-01

    The computerized brain atlas constructed at the Karolinska Hospital, Stockholm, Sweden, has been further developed. This atlas was designed to be employed in different fields of neuro imaging such as positron emission tomography (PET), single photon emission tomography (SPECT), computerized tomography (CT) and magnetic resonance imaging (MR). The main objectives with the atlas is to aid the interpretation of functional images by introducing anatomical information, to serve as a tool in the merging of data from different imaging modalities and to facilitate the comparisons of data from different individuals by allowing for anatomical standardization of individual data. The purpose of this paper is to describe the algorithms and transformations used in the implementation of the atlas software

  11. A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease.

    Science.gov (United States)

    Bardinet, Eric; Bhattacharjee, Manik; Dormont, Didier; Pidoux, Bernard; Malandain, Grégoire; Schüpbach, Michael; Ayache, Nicholas; Cornu, Philippe; Agid, Yves; Yelnik, Jérôme

    2009-02-01

    The localization of any given target in the brain has become a challenging issue because of the increased use of deep brain stimulation to treat Parkinson disease, dystonia, and nonmotor diseases (for example, Tourette syndrome, obsessive compulsive disorders, and depression). The aim of this study was to develop an automated method of adapting an atlas of the human basal ganglia to the brains of individual patients. Magnetic resonance images of the brain specimen were obtained before extraction from the skull and histological processing. Adaptation of the atlas to individual patient anatomy was performed by reshaping the atlas MR images to the images obtained in the individual patient using a hierarchical registration applied to a region of interest centered on the basal ganglia, and then applying the reshaping matrix to the atlas surfaces. Results were evaluated by direct visual inspection of the structures visible on MR images and atlas anatomy, by comparison with electrophysiological intraoperative data, and with previous atlas studies in patients with Parkinson disease. The method was both robust and accurate, never failing to provide an anatomically reliable atlas to patient registration. The registration obtained did not exceed a 1-mm mismatch with the electrophysiological signatures in the region of the subthalamic nucleus. This registration method applied to the basal ganglia atlas forms a powerful and reliable method for determining deep brain stimulation targets within the basal ganglia of individual patients.

  12. Fast and robust multi-atlas segmentation of brain magnetic resonance images

    DEFF Research Database (Denmark)

    Lötjönen, Jyrki Mp; Wolz, Robin; Koikkalainen, Juha R

    2010-01-01

    We introduce an optimised pipeline for multi-atlas brain MRI segmentation. Both accuracy and speed of segmentation are considered. We study different similarity measures used in non-rigid registration. We show that intensity differences for intensity normalised images can be used instead of stand......We introduce an optimised pipeline for multi-atlas brain MRI segmentation. Both accuracy and speed of segmentation are considered. We study different similarity measures used in non-rigid registration. We show that intensity differences for intensity normalised images can be used instead...... of standard normalised mutual information in registration without compromising the accuracy but leading to threefold decrease in the computation time. We study and validate also different methods for atlas selection. Finally, we propose two new approaches for combining multi-atlas segmentation and intensity...

  13. Practical MRI atlas of neonatal brain development

    International Nuclear Information System (INIS)

    Barkovich, A.J.; Truwit, C.L.

    1990-01-01

    This book is an anatomical reference for cranial magnetic resonance imaging (MRI) studies in neonates and infants. It contains 122 clear, sharp MRI scans and drawings showing changes in the normal appearance of the brain and skull during development. Sections of the atlas depict the major processes of maturation: brain myelination, development of the corpus callosum, development of the cranial bone marrow, and iron deposition in the brain. High-quality scans illustrate how these changes appear on magnetic resonance images during various stages of development

  14. Development of representative magnetic resonance imaging-based atlases of the canine brain and evaluation of three methods for atlas-based segmentation.

    Science.gov (United States)

    Milne, Marjorie E; Steward, Christopher; Firestone, Simon M; Long, Sam N; O'Brien, Terrence J; Moffat, Bradford A

    2016-04-01

    To develop representative MRI atlases of the canine brain and to evaluate 3 methods of atlas-based segmentation (ABS). 62 dogs without clinical signs of epilepsy and without MRI evidence of structural brain disease. The MRI scans from 44 dogs were used to develop 4 templates on the basis of brain shape (brachycephalic, mesaticephalic, dolichocephalic, and combined mesaticephalic and dolichocephalic). Atlas labels were generated by segmenting the brain, ventricular system, hippocampal formation, and caudate nuclei. The MRI scans from the remaining 18 dogs were used to evaluate 3 methods of ABS (manual brain extraction and application of a brain shape-specific template [A], automatic brain extraction and application of a brain shape-specific template [B], and manual brain extraction and application of a combined template [C]). The performance of each ABS method was compared by calculation of the Dice and Jaccard coefficients, with manual segmentation used as the gold standard. Method A had the highest mean Jaccard coefficient and was the most accurate ABS method assessed. Measures of overlap for ABS methods that used manual brain extraction (A and C) ranged from 0.75 to 0.95 and compared favorably with repeated measures of overlap for manual extraction, which ranged from 0.88 to 0.97. Atlas-based segmentation was an accurate and repeatable method for segmentation of canine brain structures. It could be performed more rapidly than manual segmentation, which should allow the application of computer-assisted volumetry to large data sets and clinical cases and facilitate neuroimaging research and disease diagnosis.

  15. Automatic structural parcellation of mouse brain MRI using multi-atlas label fusion.

    Directory of Open Access Journals (Sweden)

    Da Ma

    Full Text Available Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework.

  16. Deformably registering and annotating whole CLARITY brains to an atlas via masked LDDMM

    Science.gov (United States)

    Kutten, Kwame S.; Vogelstein, Joshua T.; Charon, Nicolas; Ye, Li; Deisseroth, Karl; Miller, Michael I.

    2016-04-01

    The CLARITY method renders brains optically transparent to enable high-resolution imaging in the structurally intact brain. Anatomically annotating CLARITY brains is necessary for discovering which regions contain signals of interest. Manually annotating whole-brain, terabyte CLARITY images is difficult, time-consuming, subjective, and error-prone. Automatically registering CLARITY images to a pre-annotated brain atlas offers a solution, but is difficult for several reasons. Removal of the brain from the skull and subsequent storage and processing cause variable non-rigid deformations, thus compounding inter-subject anatomical variability. Additionally, the signal in CLARITY images arises from various biochemical contrast agents which only sparsely label brain structures. This sparse labeling challenges the most commonly used registration algorithms that need to match image histogram statistics to the more densely labeled histological brain atlases. The standard method is a multiscale Mutual Information B-spline algorithm that dynamically generates an average template as an intermediate registration target. We determined that this method performs poorly when registering CLARITY brains to the Allen Institute's Mouse Reference Atlas (ARA), because the image histogram statistics are poorly matched. Therefore, we developed a method (Mask-LDDMM) for registering CLARITY images, that automatically finds the brain boundary and learns the optimal deformation between the brain and atlas masks. Using Mask-LDDMM without an average template provided better results than the standard approach when registering CLARITY brains to the ARA. The LDDMM pipelines developed here provide a fast automated way to anatomically annotate CLARITY images; our code is available as open source software at http://NeuroData.io.

  17. A digital 3D atlas of the marmoset brain based on multi-modal MRI.

    Science.gov (United States)

    Liu, Cirong; Ye, Frank Q; Yen, Cecil Chern-Chyi; Newman, John D; Glen, Daniel; Leopold, David A; Silva, Afonso C

    2018-04-01

    The common marmoset (Callithrix jacchus) is a New-World monkey of growing interest in neuroscience. Magnetic resonance imaging (MRI) is an essential tool to unveil the anatomical and functional organization of the marmoset brain. To facilitate identification of regions of interest, it is desirable to register MR images to an atlas of the brain. However, currently available atlases of the marmoset brain are mainly based on 2D histological data, which are difficult to apply to 3D imaging techniques. Here, we constructed a 3D digital atlas based on high-resolution ex-vivo MRI images, including magnetization transfer ratio (a T1-like contrast), T2w images, and multi-shell diffusion MRI. Based on the multi-modal MRI images, we manually delineated 54 cortical areas and 16 subcortical regions on one hemisphere of the brain (the core version). The 54 cortical areas were merged into 13 larger cortical regions according to their locations to yield a coarse version of the atlas, and also parcellated into 106 sub-regions using a connectivity-based parcellation method to produce a refined atlas. Finally, we compared the new atlas set with existing histology atlases and demonstrated its applications in connectome studies, and in resting state and stimulus-based fMRI. The atlas set has been integrated into the widely-distributed neuroimaging data analysis software AFNI and SUMA, providing a readily usable multi-modal template space with multi-level anatomical labels (including labels from the Paxinos atlas) that can facilitate various neuroimaging studies of marmosets. Published by Elsevier Inc.

  18. Subject-Specific Sparse Dictionary Learning for Atlas-Based Brain MRI Segmentation.

    Science.gov (United States)

    Roy, Snehashis; He, Qing; Sweeney, Elizabeth; Carass, Aaron; Reich, Daniel S; Prince, Jerry L; Pham, Dzung L

    2015-09-01

    Quantitative measurements from segmentations of human brain magnetic resonance (MR) images provide important biomarkers for normal aging and disease progression. In this paper, we propose a patch-based tissue classification method from MR images that uses a sparse dictionary learning approach and atlas priors. Training data for the method consists of an atlas MR image, prior information maps depicting where different tissues are expected to be located, and a hard segmentation. Unlike most atlas-based classification methods that require deformable registration of the atlas priors to the subject, only affine registration is required between the subject and training atlas. A subject-specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches leading to tissue memberships at each voxel. The combination of prior information in an example-based framework enables us to distinguish tissues having similar intensities but different spatial locations. We demonstrate the efficacy of the approach on the application of whole-brain tissue segmentation in subjects with healthy anatomy and normal pressure hydrocephalus, as well as lesion segmentation in multiple sclerosis patients. For each application, quantitative comparisons are made against publicly available state-of-the art approaches.

  19. Monitoring the injured brain: registered, patient specific atlas models to improve accuracy of recovered brain saturation values

    Science.gov (United States)

    Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J. E.; Su, Zhangjie; Dehghani, Hamid

    2015-07-01

    The subject of superficial contamination and signal origins remains a widely debated topic in the field of Near Infrared Spectroscopy (NIRS), yet the concept of using the technology to monitor an injured brain, in a clinical setting, poses additional challenges concerning the quantitative accuracy of recovered parameters. Using high density diffuse optical tomography probes, quantitatively accurate parameters from different layers (skin, bone and brain) can be recovered from subject specific reconstruction models. This study assesses the use of registered atlas models for situations where subject specific models are not available. Data simulated from subject specific models were reconstructed using the 8 registered atlas models implementing a regional (layered) parameter recovery in NIRFAST. A 3-region recovery based on the atlas model yielded recovered brain saturation values which were accurate to within 4.6% (percentage error) of the simulated values, validating the technique. The recovered saturations in the superficial regions were not quantitatively accurate. These findings highlight differences in superficial (skin and bone) layer thickness between the subject and atlas models. This layer thickness mismatch was propagated through the reconstruction process decreasing the parameter accuracy.

  20. Windows on the brain: the emerging role of atlases and databases in neuroscience

    Science.gov (United States)

    Van Essen, David C.; VanEssen, D. C. (Principal Investigator)

    2002-01-01

    Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data. Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities and internet access.

  1. Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas

    Science.gov (United States)

    Grange, Pascal

    2015-09-01

    The Allen Brain Atlas of the adult mouse (ABA) consists of digitized expression profiles of thousands of genes in the mouse brain, co-registered to a common three-dimensional template (the Allen Reference Atlas).This brain-wide, genome-wide data set has triggered a renaissance in neuroanatomy. Its voxelized version (with cubic voxels of side 200 microns) is available for desktop computation in MATLAB. On the other hand, brain cells exhibit a great phenotypic diversity (in terms of size, shape and electrophysiological activity), which has inspired the names of some well-studied cell types, such as granule cells and medium spiny neurons. However, no exhaustive taxonomy of brain cell is available. A genetic classification of brain cells is being undertaken, and some cell types have been chraracterized by their transcriptome profiles. However, given a cell type characterized by its transcriptome, it is not clear where else in the brain similar cells can be found. The ABA can been used to solve this region-specificity problem in a data-driven way: rewriting the brain-wide expression profiles of all genes in the atlas as a sum of cell-type-specific transcriptome profiles is equivalent to solving a quadratic optimization problem at each voxel in the brain. However, the estimated brain-wide densities of 64 cell types published recently were based on one series of co-registered coronal in situ hybridization (ISH) images per gene, whereas the online ABA contains several image series per gene, including sagittal ones. In the presented work, we simulate the variability of cell-type densities in a Monte Carlo way by repeatedly drawing a random image series for each gene and solving the optimization problem. This yields error bars on the region-specificity of cell types.

  2. Atlas of regional anatomy of the brain using MRI. With functional correlations

    International Nuclear Information System (INIS)

    Tamraz, J.C.

    2006-01-01

    The volume provides a unique review of the essential topographical anatomy of the brain from an MRI perspective, correlating high-quality anatomical plates with the corresponding high-resolution MRI images. The book includes a historical review of brain mapping and an analysis of the essential reference planes used for the study of the human brain. Subsequent chapters provide a detailed review of the sulcal and the gyral anatomy of the human cortex, guiding the reader through an interpretation of the individual brain atlas provided by high-resolution MRI. The relationship between brain structure and function is approached in a topographical fashion with analysis of the necessary imaging methodology and displayed anatomy. The central, perisylvian, mesial temporal and occipital areas receive special attention. Imaging of the core brain structures is included. An extensive coronal atlas concludes the book. (orig.)

  3. A combined histological and MRI brain atlas of the common marmoset monkey, Callithrix jacchus.

    Science.gov (United States)

    Newman, John D; Kenkel, William M; Aronoff, Emily C; Bock, Nicholas A; Zametkin, Molly R; Silva, Afonso C

    2009-12-11

    The common marmoset, Callithrix jacchus, is of growing importance for research in neuroscience and related fields. In the present work, we describe a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. The histological sections and a simplified schematic atlas are available online at http://udn.nichd.nih.gov/brainatlas_home.html.

  4. 7.0 tesla MRI brain white matter atlas. 2. ed.

    International Nuclear Information System (INIS)

    Cho, Zang-Hee

    2015-01-01

    Depicts the visualization of brain white matter with the latest 7.0 T MRI and TDI techniques. Represents a useful addition to brain research and clinical settings, such as the Human Connectome Project. Contains a wealth of exquisitely detailed color images. The introduction of techniques that permit visualization of the human nervous system is one of the foremost advances in neuroscience and brain-related research. Among the most recent significant developments in this respect are ultra-high field MRI and the image post-processing technique known as track density imaging (TDI). It is these techniques (including super-resolution TDI) which represent the two major components of 7.0 Tesla MRI - Brain White Matter Atlas. This second edition of the atlas has been revised and updated to fully reflect current application of these technological advancements in order to visualize the nervous system and the brain with the finest resolution and sensitivity. Exquisitely detailed color images offer neuroscientists, neurologists, and neurosurgeons a superb resource that will be of value both for the purpose of research and for the treatment of common brain diseases such as Alzheimer's disease and multiple sclerosis.

  5. 7.0 tesla MRI brain white matter atlas. 2. ed.

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Zang-Hee (ed.) [Gachon Univ., Incheon (Korea, Republic of). Neuroscience Research Institute

    2015-04-01

    Depicts the visualization of brain white matter with the latest 7.0 T MRI and TDI techniques. Represents a useful addition to brain research and clinical settings, such as the Human Connectome Project. Contains a wealth of exquisitely detailed color images. The introduction of techniques that permit visualization of the human nervous system is one of the foremost advances in neuroscience and brain-related research. Among the most recent significant developments in this respect are ultra-high field MRI and the image post-processing technique known as track density imaging (TDI). It is these techniques (including super-resolution TDI) which represent the two major components of 7.0 Tesla MRI - Brain White Matter Atlas. This second edition of the atlas has been revised and updated to fully reflect current application of these technological advancements in order to visualize the nervous system and the brain with the finest resolution and sensitivity. Exquisitely detailed color images offer neuroscientists, neurologists, and neurosurgeons a superb resource that will be of value both for the purpose of research and for the treatment of common brain diseases such as Alzheimer's disease and multiple sclerosis.

  6. Construction of a consistent high-definition spatio-temporal atlas of the developing brain using adaptive kernel regression.

    Science.gov (United States)

    Serag, Ahmed; Aljabar, Paul; Ball, Gareth; Counsell, Serena J; Boardman, James P; Rutherford, Mary A; Edwards, A David; Hajnal, Joseph V; Rueckert, Daniel

    2012-02-01

    Medical imaging has shown that, during early development, the brain undergoes more changes in size, shape and appearance than at any other time in life. A better understanding of brain development requires a spatio-temporal atlas that characterizes the dynamic changes during this period. In this paper we present an approach for constructing a 4D atlas of the developing brain, between 28 and 44 weeks post-menstrual age at time of scan, using T1 and T2 weighted MR images from 204 premature neonates. The method used for the creation of the average 4D atlas utilizes non-rigid registration between all pairs of images to eliminate bias in the atlas toward any of the original images. In addition, kernel regression is used to produce age-dependent anatomical templates. A novelty in our approach is the use of a time-varying kernel width, to overcome the variations in the distribution of subjects at different ages. This leads to an atlas that retains a consistent level of detail at every time-point. Comparisons between the resulting atlas and atlases constructed using affine and non-rigid registration are presented. The resulting 4D atlas has greater anatomic definition than currently available 4D atlases created using various affine and non-rigid registration approaches, an important factor in improving registrations between the atlas and individual subjects. Also, the resulting 4D atlas can serve as a good representative of the population of interest as it reflects both global and local changes. The atlas is publicly available at www.brain-development.org. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Sources of variation influencing concordance between functional MRI and direct cortical stimulation in brain tumor surgery

    Directory of Open Access Journals (Sweden)

    Melanie A Morrison

    2016-10-01

    Full Text Available Object: Preoperative functional magnetic resonance imaging (fMRI remains a promising method to aid in the surgical management of patients diagnosed with brain tumors. For patients that are candidates for awake craniotomies, surgical decisions can potentially be improved by fMRI but this depends on the level of concordance between preoperative brain maps and the maps provided by the gold standard intraoperative method, direct cortical stimulation (DCS. There have been numerous studies of the concordance between fMRI and DCS using sensitivity and specificity measures, however the results are variable across studies and the key factors influencing variability are not well understood. Thus, the present work addresses the influence of technical factors on fMRI and DCS concordance. Methods: Motor and language mapping data were collected for a group of glioma patients (n = 14 who underwent both preoperative fMRI and intraoperative DCS in an awake craniotomy procedure for tumor removal. Normative fMRI data were also acquired in a healthy control group (n = 12. The fMRI and DCS mapping data were co-registered; true positive (TP, true negative (TN, false positive (FP and false negative (FN occurrences were tabulated over the exposed brain surface. Sensitivity and specificity were measured for the total group, and the motor and language sub-groups. The influence of grid placement, fMRI statistical thresholding, and task standardization were assessed. Correlations between proportions of agreement and error were carefully scrutinized to evaluate concordance more in-depth. Results: Concordance was significantly better for motor versus language mapping. There was an inverse relationship between TP and TN with increasing statistical threshold, and FP dominated the total error. Sensitivity and specificity were reduced when tasks were not standardized across fMRI and DCS. Conclusions: Although the agreement between fMRI and DCS is good, variability is introduced

  8. A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei.

    Science.gov (United States)

    Pauli, Wolfgang M; Nili, Amanda N; Tyszka, J Michael

    2018-04-17

    Recent advances in magnetic resonance imaging methods, including data acquisition, pre-processing and analysis, have benefited research on the contributions of subcortical brain nuclei to human cognition and behavior. At the same time, these developments have led to an increasing need for a high-resolution probabilistic in vivo anatomical atlas of subcortical nuclei. In order to address this need, we constructed high spatial resolution, three-dimensional templates, using high-accuracy diffeomorphic registration of T 1 - and T 2 - weighted structural images from 168 typical adults between 22 and 35 years old. In these templates, many tissue boundaries are clearly visible, which would otherwise be impossible to delineate in data from individual studies. The resulting delineations of subcortical nuclei complement current histology-based atlases. We further created a companion library of software tools for atlas development, to offer an open and evolving resource for the creation of a crowd-sourced in vivo probabilistic anatomical atlas of the human brain.

  9. Brain Atlas Fusion from High-Thickness Diagnostic Magnetic Resonance Images by Learning-Based Super-Resolution.

    Science.gov (United States)

    Zhang, Jinpeng; Zhang, Lichi; Xiang, Lei; Shao, Yeqin; Wu, Guorong; Zhou, Xiaodong; Shen, Dinggang; Wang, Qian

    2017-03-01

    It is fundamentally important to fuse the brain atlas from magnetic resonance (MR) images for many imaging-based studies. Most existing works focus on fusing the atlases from high-quality MR images. However, for low-quality diagnostic images (i.e., with high inter-slice thickness), the problem of atlas fusion has not been addressed yet. In this paper, we intend to fuse the brain atlas from the high-thickness diagnostic MR images that are prevalent for clinical routines. The main idea of our works is to extend the conventional groupwise registration by incorporating a novel super-resolution strategy. The contribution of the proposed super-resolution framework is two-fold. First, each high-thickness subject image is reconstructed to be isotropic by the patch-based sparsity learning. Then, the reconstructed isotropic image is enhanced for better quality through the random-forest-based regression model. In this way, the images obtained by the super-resolution strategy can be fused together by applying the groupwise registration method to construct the required atlas. Our experiments have shown that the proposed framework can effectively solve the problem of atlas fusion from the low-quality brain MR images.

  10. Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool.

    Science.gov (United States)

    Zaldivar, Andrew; Krichmar, Jeffrey L

    2014-01-01

    The Allen Brain Atlas-Driven Visualizations (ABADV) is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA) across multiple genes and brain structures. Though the ABA offers their own search engine and software for researchers to view their growing collection of online public data sets, including extensive gene expression and neuroanatomical data from human and mouse brain, many of their tools limit the amount of genes and brain structures researchers can view at once. To complement their work, ABADV generates multiple pie charts, bar charts and heat maps of expression energy values for any given set of genes and brain structures. Such a suite of free and easy-to-understand visualizations allows for easy comparison of gene expression across multiple brain areas. In addition, each visualization links back to the ABA so researchers may view a summary of the experimental detail. ABADV is currently supported on modern web browsers and is compatible with expression energy data from the Allen Mouse Brain Atlas in situ hybridization data. By creating this web application, researchers can immediately obtain and survey numerous amounts of expression energy data from the ABA, which they can then use to supplement their work or perform meta-analysis. In the future, we hope to enable ABADV across multiple data resources.

  11. Allen Brain Atlas-Driven Visualizations: A Web-Based Gene Expression Energy Visualization Tool

    Directory of Open Access Journals (Sweden)

    Andrew eZaldivar

    2014-05-01

    Full Text Available The Allen Brain Atlas-Driven Visualizations (ABADV is a publicly accessible web-based tool created to retrieve and visualize expression energy data from the Allen Brain Atlas (ABA across multiple genes and brain structures. Though the ABA offers their own search engine and software for researchers to view their growing collection of online public data sets, including extensive gene expression and neuroanatomical data from human and mouse brain, many of their tools limit the amount of genes and brain structures researchers can view at once. To complement their work, ABADV generates multiple pie charts, bar charts and heat maps of expression energy values for any given set of genes and brain structures. Such a suite of free and easy-to-understand visualizations allows for easy comparison of gene expression across multiple brain areas. In addition, each visualization links back to the ABA so researchers may view a summary of the experimental detail. ABADV is currently supported on modern web browsers and is compatible with expression energy data from the Allen Mouse Brain Atlas in situ hybridization data. By creating this web application, researchers can immediately obtain and survey numerous amounts of expression energy data from the ABA, which they can then use to supplement their work or perform meta-analysis. In the future, we hope to enable ABADV across multiple data resources.

  12. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases.

    Science.gov (United States)

    Forbes, Jessica L; Kim, Regina E Y; Paulsen, Jane S; Johnson, Hans J

    2016-01-01

    The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%.

  13. A study of the application of Brain Atlas with and without +Gz acceleration conditions.

    Science.gov (United States)

    Li, Yifeng; Zhang, Lihui; Zhang, Tao; Li, Baohui

    2017-07-20

    The purposes of this study were to utilize Brain Atlas to investigate the fluctuations in the characteristics of human EEG, with and without +Gz acceleration produced by human centrifuge, and also to examine the G load endurance of human body. The Brain Atlas of the EEG signal with and without +Gz acceleration in a static state were compared in order to reveal the correlation and differences. When compared with those in a static state, it was found that for the EEG readings of the subjects undergoing +Gz acceleration conditions, the energy and gray scale values of the low-frequency component-delta rhythm showed significant increases, while the energy and gray scale values of the high-frequency component-beta rhythm showed significant decreases. Among these, the beta2 rhythm was determined to be significantly inhibited. These fluctuations suggested that the ischemia conditions of brain had been improved. Also, the recoveries in the energy and gray-scale values were determined to be faster, which suggested that the G load endurance of human body had been enhanced. The Brain Atlas was found to show observable changes in color. The experimental results indicated that the Brain Atlas was able to provide assistance during the exploration of the fluctuations in the characteristics of EEG, and provided a criterion to assist in the observations of the function state fluctuations of human brain with +Gz acceleration. It also assisted in the evaluations of the G load endurance of human body.

  14. A multi-atlas based method for automated anatomical rat brain MRI segmentation and extraction of PET activity.

    Science.gov (United States)

    Lancelot, Sophie; Roche, Roxane; Slimen, Afifa; Bouillot, Caroline; Levigoureux, Elise; Langlois, Jean-Baptiste; Zimmer, Luc; Costes, Nicolas

    2014-01-01

    Preclinical in vivo imaging requires precise and reproducible delineation of brain structures. Manual segmentation is time consuming and operator dependent. Automated segmentation as usually performed via single atlas registration fails to account for anatomo-physiological variability. We present, evaluate, and make available a multi-atlas approach for automatically segmenting rat brain MRI and extracting PET activies. High-resolution 7T 2DT2 MR images of 12 Sprague-Dawley rat brains were manually segmented into 27-VOI label volumes using detailed protocols. Automated methods were developed with 7/12 atlas datasets, i.e. the MRIs and their associated label volumes. MRIs were registered to a common space, where an MRI template and a maximum probability atlas were created. Three automated methods were tested: 1/registering individual MRIs to the template, and using a single atlas (SA), 2/using the maximum probability atlas (MP), and 3/registering the MRIs from the multi-atlas dataset to an individual MRI, propagating the label volumes and fusing them in individual MRI space (propagation & fusion, PF). Evaluation was performed on the five remaining rats which additionally underwent [18F]FDG PET. Automated and manual segmentations were compared for morphometric performance (assessed by comparing volume bias and Dice overlap index) and functional performance (evaluated by comparing extracted PET measures). Only the SA method showed volume bias. Dice indices were significantly different between methods (PF>MP>SA). PET regional measures were more accurate with multi-atlas methods than with SA method. Multi-atlas methods outperform SA for automated anatomical brain segmentation and PET measure's extraction. They perform comparably to manual segmentation for FDG-PET quantification. Multi-atlas methods are suitable for rapid reproducible VOI analyses.

  15. Whole-brain activity mapping onto a zebrafish brain atlas.

    Science.gov (United States)

    Randlett, Owen; Wee, Caroline L; Naumann, Eva A; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E; Portugues, Ruben; Lacoste, Alix M B; Riegler, Clemens; Engert, Florian; Schier, Alexander F

    2015-11-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal–regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors.

  16. Whole-brain activity mapping onto a zebrafish brain atlas

    Science.gov (United States)

    Randlett, Owen; Wee, Caroline L.; Naumann, Eva A.; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E.; Portugues, Ruben; Lacoste, Alix M.B.; Riegler, Clemens; Engert, Florian; Schier, Alexander F.

    2015-01-01

    In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open source atlas containing molecular labels and anatomical region definitions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated-Extracellular signal-regulated kinase (ERK/MAPK) as a readout of neural activity, we have developed a system to create and contextualize whole brain maps of stimulus- and behavior-dependent neural activity. This MAP-Mapping (Mitogen Activated Protein kinase – Mapping) assay is technically simple, fast, inexpensive, and data analysis is completely automated. Since MAP-Mapping is performed on fish that are freely swimming, it is applicable to nearly any stimulus or behavior. We demonstrate the utility of our high-throughput approach using hunting/feeding, pharmacological, visual and noxious stimuli. The resultant maps outline hundreds of areas associated with behaviors. PMID:26778924

  17. Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood.

    Science.gov (United States)

    Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G; Anblagan, Devasuda; Telford, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Macnaught, Gillian; Semple, Scott I; Bastin, Mark E; Boardman, James P

    2016-01-01

    Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39(+5) weeks, range 37(+2)-41(+6)). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development.

  18. Parcellation of the healthy neonatal brain into 107 regions using atlas propagation through intermediate time points in childhood

    Directory of Open Access Journals (Sweden)

    Manuel eBlesa Cabez

    2016-05-01

    Full Text Available Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39+5 weeks, range 37+2-41+6. An adult brain atlas (SRI24/TZO was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database, with the final atlas (Edinburgh Neonatal Atlas, ENA33 constructed using the Symmetric Group Normalization method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modelling brain growth during development.

  19. Constructing fine-granularity functional brain network atlases via deep convolutional autoencoder.

    Science.gov (United States)

    Zhao, Yu; Dong, Qinglin; Chen, Hanbo; Iraji, Armin; Li, Yujie; Makkie, Milad; Kou, Zhifeng; Liu, Tianming

    2017-12-01

    State-of-the-art functional brain network reconstruction methods such as independent component analysis (ICA) or sparse coding of whole-brain fMRI data can effectively infer many thousands of volumetric brain network maps from a large number of human brains. However, due to the variability of individual brain networks and the large scale of such networks needed for statistically meaningful group-level analysis, it is still a challenging and open problem to derive group-wise common networks as network atlases. Inspired by the superior spatial pattern description ability of the deep convolutional neural networks (CNNs), a novel deep 3D convolutional autoencoder (CAE) network is designed here to extract spatial brain network features effectively, based on which an Apache Spark enabled computational framework is developed for fast clustering of larger number of network maps into fine-granularity atlases. To evaluate this framework, 10 resting state networks (RSNs) were manually labeled from the sparsely decomposed networks of Human Connectome Project (HCP) fMRI data and 5275 network training samples were obtained, in total. Then the deep CAE models are trained by these functional networks' spatial maps, and the learned features are used to refine the original 10 RSNs into 17 network atlases that possess fine-granularity functional network patterns. Interestingly, it turned out that some manually mislabeled outliers in training networks can be corrected by the deep CAE derived features. More importantly, fine granularities of networks can be identified and they reveal unique network patterns specific to different brain task states. By further applying this method to a dataset of mild traumatic brain injury study, it shows that the technique can effectively identify abnormal small networks in brain injury patients in comparison with controls. In general, our work presents a promising deep learning and big data analysis solution for modeling functional connectomes, with

  20. A multi-atlas based method for automated anatomical Macaca fascicularis brain MRI segmentation and PET kinetic extraction.

    Science.gov (United States)

    Ballanger, Bénédicte; Tremblay, Léon; Sgambato-Faure, Véronique; Beaudoin-Gobert, Maude; Lavenne, Franck; Le Bars, Didier; Costes, Nicolas

    2013-08-15

    MRI templates and digital atlases are needed for automated and reproducible quantitative analysis of non-human primate PET studies. Segmenting brain images via multiple atlases outperforms single-atlas labelling in humans. We present a set of atlases manually delineated on brain MRI scans of the monkey Macaca fascicularis. We use this multi-atlas dataset to evaluate two automated methods in terms of accuracy, robustness and reliability in segmenting brain structures on MRI and extracting regional PET measures. Twelve individual Macaca fascicularis high-resolution 3DT1 MR images were acquired. Four individual atlases were created by manually drawing 42 anatomical structures, including cortical and sub-cortical structures, white matter regions, and ventricles. To create the MRI template, we first chose one MRI to define a reference space, and then performed a two-step iterative procedure: affine registration of individual MRIs to the reference MRI, followed by averaging of the twelve resampled MRIs. Automated segmentation in native space was obtained in two ways: 1) Maximum probability atlases were created by decision fusion of two to four individual atlases in the reference space, and transformation back into the individual native space (MAXPROB)(.) 2) One to four individual atlases were registered directly to the individual native space, and combined by decision fusion (PROPAG). Accuracy was evaluated by computing the Dice similarity index and the volume difference. The robustness and reproducibility of PET regional measurements obtained via automated segmentation was evaluated on four co-registered MRI/PET datasets, which included test-retest data. Dice indices were always over 0.7 and reached maximal values of 0.9 for PROPAG with all four individual atlases. There was no significant mean volume bias. The standard deviation of the bias decreased significantly when increasing the number of individual atlases. MAXPROB performed better when increasing the number of

  1. Comparing the Expression of Genes Related to Serotonin (5-HT in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain Atlas

    Directory of Open Access Journals (Sweden)

    C. A. Acevedo-Triana

    2017-01-01

    Full Text Available Brain atlases are tools based on comprehensive studies used to locate biological characteristics (structures, connections, proteins, and gene expression in different regions of the brain. These atlases have been disseminated to the point where tools have been created to store, manage, and share the information they contain. This study used the data published by the Allen Mouse Brain Atlas (2004 for mice (C57BL/6J and Allen Human Brain Atlas (2010 for humans (6 donors to compare the expression of serotonin-related genes. Genes of interest were searched for manually in each case (in situ hybridization for mice and microarrays for humans, normalized expression data (z-scores were extracted, and the results were graphed. Despite the differences in methodology, quantification, and subjects used in the process, a high degree of similarity was found between expression data. Here we compare expression in a way that allows the use of translational research methods to infer and validate knowledge. This type of study allows part of the relationship between structures and functions to be identified, by examining expression patterns and comparing levels of expression in different states, anatomical correlations, and phenotypes between different species. The study concludes by discussing the importance of knowing, managing, and disseminating comprehensive, open-access studies in neuroscience.

  2. A Customizable MR Brain Imaging Atlas of Structure and Function for Decision Support.

    Science.gov (United States)

    U., Sinha; S., El-Saden; G., Duckwiler; L., Thompson; S., Ardekani; H., Kangarloo

    2003-01-01

    We present a MR brain atlas for structure and function (diffusion weighted images). The atlas is customizable for contrast and orientation to match the current patient images. In addition, the atlas also provides normative values of MR parameters. The atlas is designed on informatics principles to provide context sensitive decision support at the time of primary image interpretation. Additional support for diagnostic interpretation is provided by a list of expert created most relevant ‘Image Finding Descriptors’ that will serve as cues to the user. The architecture of the atlas module is integrated into the image workflow of a radiology department to provide support at the time of primary diagnosis. PMID:14728244

  3. A three-dimensional MRI atlas of the zebra finch brain in stereotaxic coordinates

    DEFF Research Database (Denmark)

    Poirier, Colline; Vellema, Michiel; Verhoye, Marleen

    2008-01-01

    of different brain areas (nuclei) involved in the sensory and motor control of song. Until now, the only published atlases of songbird brains consisted in drawings based on histological slices of the canary and of the zebra finch brain. Taking advantage of high-magnetic field (7 Tesla) MRI technique, we...

  4. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

    Science.gov (United States)

    Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

    2014-03-01

    The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

  5. Nonlocal atlas-guided multi-channel forest learning for human brain labeling.

    Science.gov (United States)

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2016-02-01

    It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. The authors have comprehensively evaluated their method on both public LONI_LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the dice similarity coefficient

  6. Computation of a high-resolution MRI 3D stereotaxic atlas of the sheep brain.

    Science.gov (United States)

    Ella, Arsène; Delgadillo, José A; Chemineau, Philippe; Keller, Matthieu

    2017-02-15

    The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1-weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high-resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676-692, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Rat brain digital stereotaxic white matter atlas with fine tract delineation in Paxinos space and its automated applications in DTI data analysis.

    Science.gov (United States)

    Liang, Shengxiang; Wu, Shang; Huang, Qi; Duan, Shaofeng; Liu, Hua; Li, Yuxiao; Zhao, Shujun; Nie, Binbin; Shan, Baoci

    2017-11-01

    To automatically analyze diffusion tensor images of the rat brain via both voxel-based and ROI-based approaches, we constructed a new white matter atlas of the rat brain with fine tracts delineation in the Paxinos and Watson space. Unlike in previous studies, we constructed a digital atlas image from the latest edition of the Paxinos and Watson. This atlas contains 111 carefully delineated white matter fibers. A white matter network of rat brain based on anatomy was constructed by locating the intersection of all these tracts and recording the nuclei on the pathway of each white matter tract. Moreover, a compatible rat brain template from DTI images was created and standardized into the atlas space. To evaluate the automated application of the atlas in DTI data analysis, a group of rats with right-side middle cerebral artery occlusion (MCAO) and those without were enrolled in this study. The voxel-based analysis result shows that the brain region showing significant declines in signal in the MCAO rats was consistent with the occlusion position. We constructed a stereotaxic white matter atlas of the rat brain with fine tract delineation and a compatible template for the data analysis of DTI images of the rat brain. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Three-dimensional stereotactic atlas of the adult human skull correlated with the brain, cranial nerves, and intracranial vasculature.

    Science.gov (United States)

    Nowinski, Wieslaw L; Thaung, Thant Shoon Let; Chua, Beng Choon; Yi, Su Hnin Wut; Ngai, Vincent; Yang, Yili; Chrzan, Robert; Urbanik, Andrzej

    2015-05-15

    Although the adult human skull is a complex and multifunctional structure, its 3D, complete, realistic, and stereotactic atlas has not yet been created. This work addresses the construction of a 3D interactive atlas of the adult human skull spatially correlated with the brain, cranial nerves, and intracranial vasculature. The process of atlas construction included computed tomography (CT) high-resolution scan acquisition, skull extraction, skull parcellation, 3D disarticulated bone surface modeling, 3D model simplification, brain-skull registration, 3D surface editing, 3D surface naming and color-coding, integration of the CT-derived 3D bony models with the existing brain atlas, and validation. The virtual skull model created is complete with all 29 bones, including the auditory ossicles (being among the smallest bones). It contains all typical bony features and landmarks. The created skull model is superior to the existing skull models in terms of completeness, realism, and integration with the brain along with blood vessels and cranial nerves. This skull atlas is valuable for medical students and residents to easily get familiarized with the skull and surrounding anatomy with a few clicks. The atlas is also useful for educators to prepare teaching materials. It may potentially serve as a reference aid in the reading and operating rooms. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Robust methods to create ex vivo minimum deformation atlases for brain mapping.

    Science.gov (United States)

    Janke, Andrew L; Ullmann, Jeremy F P

    2015-02-01

    Highly detailed ex vivo 3D atlases of average structure are of critical importance to neuroscience and its current push to understanding the global microstructure of the brain. Multiple single slice histology sections can no longer provide sufficient detail of inter-slice microstructure and lack out of plane resolution. Two ex vivo methods have emerged that can create such detailed models. High-field micro MRI with the addition of contrast media has allowed intact whole brain microstructure imaging with an isotropic resolution of 15 μm in mouse. Blockface imaging has similarly evolved to a point where it is now possible to image an entire brain in a rigorous fashion with an out of plane resolution of 10 μm. Despite the destruction of the tissue as part of this process it allows a reconstructed model that is free from cutting artifacts. Both of these methods have been utilised to create minimum deformation atlases that are representative of the respective populations. The MDA atlases allow us unprecedented insight into the commonality and differences in microstructure in cortical structures in specific taxa. In this paper we provide an overview of how to create such MDA models from ex vivo data. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. A human brain atlas derived via n-cut parcellation of resting-state and task-based fMRI data.

    Science.gov (United States)

    James, George Andrew; Hazaroglu, Onder; Bush, Keith A

    2016-02-01

    The growth of functional MRI has led to development of human brain atlases derived by parcellating resting-state connectivity patterns into functionally independent regions of interest (ROIs). All functional atlases to date have been derived from resting-state fMRI data. But given that functional connectivity between regions varies with task, we hypothesized that an atlas incorporating both resting-state and task-based fMRI data would produce an atlas with finer characterization of task-relevant regions than an atlas derived from resting-state alone. To test this hypothesis, we derived parcellation atlases from twenty-nine healthy adult participants enrolled in the Cognitive Connectome project, an initiative to improve functional MRI's translation into clinical decision-making by mapping normative variance in brain-behavior relationships. Participants underwent resting-state and task-based fMRI spanning nine cognitive domains: motor, visuospatial, attention, language, memory, affective processing, decision-making, working memory, and executive function. Spatially constrained n-cut parcellation derived brain atlases using (1) all participants' functional data (Task) or (2) a single resting-state scan (Rest). An atlas was also derived from random parcellation for comparison purposes (Random). Two methods were compared: (1) a parcellation applied to the group's mean edge weights (mean), and (2) a two-stage approach with parcellation of individual edge weights followed by parcellation of mean binarized edges (two-stage). The resulting Task and Rest atlases had significantly greater similarity with each other (mean Jaccard indices JI=0.72-0.85) than with the Random atlases (JI=0.59-0.63; all pRest atlas similarity was greatest for the two-stage method (JI=0.85), which has been shown as more robust than the mean method; these atlases also better reproduced voxelwise seed maps of the left dorsolateral prefrontal cortex during rest and performing the n-back working memory

  11. Multidimensional MRI-CT atlas of the naked mole-rat brain

    Directory of Open Access Journals (Sweden)

    Fumiko eSeki

    2013-12-01

    Full Text Available Naked mole-rats have a variety of distinctive features such as the organisation of a hierarchical society (known as eusociality, extraordinary longevity, and cancer resistance; thus, it would be worthwhile investigating these animals in detail. One important task is the preparation of a brain atlas database that provide comprehensive information containing multidimensional data with various image contrasts, which can be achievable using a magnetic resonance imaging (MRI. Advanced MRI techniques such as diffusion tensor imaging (DTI, which generates high contrast images of fibre structures, can characterise unique morphological properties in addition to conventional MRI. To obtain high spatial resolution images, MR histology, DTI, and X-ray computed tomography (CT were performed on the fixed adult brain. Skull and brain structures were segmented as well as reconstructed in stereotaxic coordinates. Data were also acquired for the neonatal brain to allow developmental changes to be observed. Moreover, in vivo imaging of naked mole-rats was established as an evaluation tool of live animals. The data obtained comprised three-dimensional (3D images with high tissue contrast as well as stereotaxic coordinates. Developmental differences in the visual system were highlighted in particular by DTI. Although it was difficult to delineate optic nerves in the mature adult brain, parts of them could be distinguished in the immature neonatal brain. From observation of cortical thickness, possibility of high somatosensory system development replaced to the visual system was indicated. 3D visualisation of brain structures in the atlas as well as the establishment of in vivo imaging would promote neuroimaging researches towards detection of novel characteristics of eusocial naked mole-rats.

  12. Multi-atlas attenuation correction supports full quantification of static and dynamic brain PET data in PET-MR

    Science.gov (United States)

    Mérida, Inés; Reilhac, Anthonin; Redouté, Jérôme; Heckemann, Rolf A.; Costes, Nicolas; Hammers, Alexander

    2017-04-01

    In simultaneous PET-MR, attenuation maps are not directly available. Essential for absolute radioactivity quantification, they need to be derived from MR or PET data to correct for gamma photon attenuation by the imaged object. We evaluate a multi-atlas attenuation correction method for brain imaging (MaxProb) on static [18F]FDG PET and, for the first time, on dynamic PET, using the serotoninergic tracer [18F]MPPF. A database of 40 MR/CT image pairs (atlases) was used. The MaxProb method synthesises subject-specific pseudo-CTs by registering each atlas to the target subject space. Atlas CT intensities are then fused via label propagation and majority voting. Here, we compared these pseudo-CTs with the real CTs in a leave-one-out design, contrasting the MaxProb approach with a simplified single-atlas method (SingleAtlas). We evaluated the impact of pseudo-CT accuracy on reconstructed PET images, compared to PET data reconstructed with real CT, at the regional and voxel levels for the following: radioactivity images; time-activity curves; and kinetic parameters (non-displaceable binding potential, BPND). On static [18F]FDG, the mean bias for MaxProb ranged between 0 and 1% for 73 out of 84 regions assessed, and exceptionally peaked at 2.5% for only one region. Statistical parametric map analysis of MaxProb-corrected PET data showed significant differences in less than 0.02% of the brain volume, whereas SingleAtlas-corrected data showed significant differences in 20% of the brain volume. On dynamic [18F]MPPF, most regional errors on BPND ranged from -1 to  +3% (maximum bias 5%) for the MaxProb method. With SingleAtlas, errors were larger and had higher variability in most regions. PET quantification bias increased over the duration of the dynamic scan for SingleAtlas, but not for MaxProb. We show that this effect is due to the interaction of the spatial tracer-distribution heterogeneity variation over time with the degree of accuracy of the attenuation maps. This

  13. Population-averaged macaque brain atlas with high-resolution ex vivo DTI integrated into in vivo space.

    Science.gov (United States)

    Feng, Lei; Jeon, Tina; Yu, Qiaowen; Ouyang, Minhui; Peng, Qinmu; Mishra, Virendra; Pletikos, Mihovil; Sestan, Nenad; Miller, Michael I; Mori, Susumu; Hsiao, Steven; Liu, Shuwei; Huang, Hao

    2017-12-01

    Animal models of the rhesus macaque (Macaca mulatta), the most widely used nonhuman primate, have been irreplaceable in neurobiological studies. However, a population-averaged macaque brain diffusion tensor imaging (DTI) atlas, including comprehensive gray and white matter labeling as well as bony and facial landmarks guiding invasive experimental procedures, is not available. The macaque white matter tract pathways and microstructures have been rarely recorded. Here, we established a population-averaged macaque brain atlas with high-resolution ex vivo DTI integrated into in vivo space incorporating bony and facial landmarks, and delineated microstructures and three-dimensional pathways of major white matter tracts in vivo MRI/DTI and ex vivo (postmortem) DTI of ten rhesus macaque brains were acquired. Single-subject macaque brain DTI template was obtained by transforming the postmortem high-resolution DTI data into in vivo space. Ex vivo DTI of ten macaque brains was then averaged in the in vivo single-subject template space to generate population-averaged macaque brain DTI atlas. The white matter tracts were traced with DTI-based tractography. One hundred and eighteen neural structures including all cortical gyri, white matter tracts and subcortical nuclei, were labeled manually on population-averaged DTI-derived maps. The in vivo microstructural metrics of fractional anisotropy, axial, radial and mean diffusivity of the traced white matter tracts were measured. Population-averaged digital atlas integrated into in vivo space can be used to label the experimental macaque brain automatically. Bony and facial landmarks will be available for guiding invasive procedures. The DTI metric measurements offer unique insights into heterogeneous microstructural profiles of different white matter tracts.

  14. Research on segmentation based on multi-atlas in brain MR image

    Science.gov (United States)

    Qian, Yuejing

    2018-03-01

    Accurate segmentation of specific tissues in brain MR image can be effectively achieved with the multi-atlas-based segmentation method, and the accuracy mainly depends on the image registration accuracy and fusion scheme. This paper proposes an automatic segmentation method based on the multi-atlas for brain MR image. Firstly, to improve the registration accuracy in the area to be segmented, we employ a target-oriented image registration method for the refinement. Then In the label fusion, we proposed a new algorithm to detect the abnormal sparse patch and simultaneously abandon the corresponding abnormal sparse coefficients, this method is made based on the remaining sparse coefficients combined with the multipoint label estimator strategy. The performance of the proposed method was compared with those of the nonlocal patch-based label fusion method (Nonlocal-PBM), the sparse patch-based label fusion method (Sparse-PBM) and majority voting method (MV). Based on our experimental results, the proposed method is efficient in the brain MR images segmentation compared with MV, Nonlocal-PBM, and Sparse-PBM methods.

  15. Applying Amide Proton Transfer MR Imaging to Hybrid Brain PET/MR: Concordance with Gadolinium Enhancement and Added Value to [18F]FDG PET.

    Science.gov (United States)

    Sun, Hongzan; Xin, Jun; Zhou, Jinyuan; Lu, Zaiming; Guo, Qiyong

    2018-06-01

    The purpose of this study is to evaluate the diagnostic concordance and metric correlations of amide proton transfer (APT) imaging with gadolinium-enhanced magnetic resonance imaging (MRI) and 2-deoxy-2-[ 18 F-]fluoro-D-glucose ([ 18 F]FDG) positron emission tomography (PET), using hybrid brain PET/MRI. Twenty-one subjects underwent brain gadolinium-enhanced [ 18 F]FDG PET/MRI prospectively. Imaging accuracy was compared between unenhanced MRI, MRI with enhancement, APT-weighted (APTW) images, and PET based on six diagnostic criteria. Among tumors, the McNemar test was further used for concordance assessment between gadolinium-enhanced imaging, APT imaging, and [ 18 F]FDG PET. As well, the relation of metrics between APT imaging and PET was analyzed by the Pearson correlation analysis. APT imaging and gadolinium-enhanced MRI showed superior and similar diagnostic accuracy. APTW signal intensity and gadolinium enhancement were concordant in 19 tumors (100 %), while high [ 18 F]FDG avidity was shown in only 12 (63.2 %). For the metrics from APT imaging and PET, there was significant correlation for 13 hypermetabolic tumors (P PET in the evaluation of tumor metabolic activity during brain PET/MR studies.

  16. Nonlocal atlas-guided multi-channel forest learning for human brain labeling

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Guangkai [Space Control and Inertial Technology Research Center, Harbin Institute of Technology, Harbin 150001, China and Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 (United States); Gao, Yaozong; Wu, Guorong [Department of Computer Science, Department of Radiology, and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 (United States); Wu, Ligang [Space Control and Inertial Technology Research Center, Harbin Institute of Technology, Harbin 150001 (China); Shen, Dinggang, E-mail: dgshen@med.unc.edu [Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and Department of Brain and Cognitive Engineering, Korea University, Seoul 02841 (Korea, Republic of)

    2016-02-15

    Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI-LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the

  17. Nonlocal atlas-guided multi-channel forest learning for human brain labeling

    International Nuclear Information System (INIS)

    Ma, Guangkai; Gao, Yaozong; Wu, Guorong; Wu, Ligang; Shen, Dinggang

    2016-01-01

    Purpose: It is important for many quantitative brain studies to label meaningful anatomical regions in MR brain images. However, due to high complexity of brain structures and ambiguous boundaries between different anatomical regions, the anatomical labeling of MR brain images is still quite a challenging task. In many existing label fusion methods, appearance information is widely used. However, since local anatomy in the human brain is often complex, the appearance information alone is limited in characterizing each image point, especially for identifying the same anatomical structure across different subjects. Recent progress in computer vision suggests that the context features can be very useful in identifying an object from a complex scene. In light of this, the authors propose a novel learning-based label fusion method by using both low-level appearance features (computed from the target image) and high-level context features (computed from warped atlases or tentative labeling maps of the target image). Methods: In particular, the authors employ a multi-channel random forest to learn the nonlinear relationship between these hybrid features and target labels (i.e., corresponding to certain anatomical structures). Specifically, at each of the iterations, the random forest will output tentative labeling maps of the target image, from which the authors compute spatial label context features and then use in combination with original appearance features of the target image to refine the labeling. Moreover, to accommodate the high inter-subject variations, the authors further extend their learning-based label fusion to a multi-atlas scenario, i.e., they train a random forest for each atlas and then obtain the final labeling result according to the consensus of results from all atlases. Results: The authors have comprehensively evaluated their method on both public LONI-LBPA40 and IXI datasets. To quantitatively evaluate the labeling accuracy, the authors use the

  18. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.

    Science.gov (United States)

    Ecker, Joseph R; Geschwind, Daniel H; Kriegstein, Arnold R; Ngai, John; Osten, Pavel; Polioudakis, Damon; Regev, Aviv; Sestan, Nenad; Wickersham, Ian R; Zeng, Hongkui

    2017-11-01

    A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability.

    Science.gov (United States)

    Calabrese, Evan; Badea, Alexandra; Watson, Charles; Johnson, G Allan

    2013-05-01

    There has been growing interest in the role of postnatal brain development in the etiology of several neurologic diseases. The rat has long been recognized as a powerful model system for studying neuropathology and the safety of pharmacologic treatments. However, the complex spatiotemporal changes that occur during rat neurodevelopment remain to be elucidated. This work establishes the first magnetic resonance histology (MRH) atlas of the developing rat brain, with an emphasis on quantitation. The atlas comprises five specimens at each of nine time points, imaged with eight distinct MR contrasts and segmented into 26 developmentally defined brain regions. The atlas was used to establish a timeline of morphometric changes and variability throughout neurodevelopment and represents a quantitative database of rat neurodevelopment for characterizing rat models of human neurologic disease. Published by Elsevier Inc.

  20. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods.

    Science.gov (United States)

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Wilkinson, A G; Macnaught, Gillian; Semple, Scott I; Boardman, James P

    2016-03-24

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.

  1. A Hybrid Hierarchical Approach for Brain Tissue Segmentation by Combining Brain Atlas and Least Square Support Vector Machine

    Science.gov (United States)

    Kasiri, Keyvan; Kazemi, Kamran; Dehghani, Mohammad Javad; Helfroush, Mohammad Sadegh

    2013-01-01

    In this paper, we present a new semi-automatic brain tissue segmentation method based on a hybrid hierarchical approach that combines a brain atlas as a priori information and a least-square support vector machine (LS-SVM). The method consists of three steps. In the first two steps, the skull is removed and the cerebrospinal fluid (CSF) is extracted. These two steps are performed using the toolbox FMRIB's automated segmentation tool integrated in the FSL software (FSL-FAST) developed in Oxford Centre for functional MRI of the brain (FMRIB). Then, in the third step, the LS-SVM is used to segment grey matter (GM) and white matter (WM). The training samples for LS-SVM are selected from the registered brain atlas. The voxel intensities and spatial positions are selected as the two feature groups for training and test. SVM as a powerful discriminator is able to handle nonlinear classification problems; however, it cannot provide posterior probability. Thus, we use a sigmoid function to map the SVM output into probabilities. The proposed method is used to segment CSF, GM and WM from the simulated magnetic resonance imaging (MRI) using Brainweb MRI simulator and real data provided by Internet Brain Segmentation Repository. The semi-automatically segmented brain tissues were evaluated by comparing to the corresponding ground truth. The Dice and Jaccard similarity coefficients, sensitivity and specificity were calculated for the quantitative validation of the results. The quantitative results show that the proposed method segments brain tissues accurately with respect to corresponding ground truth. PMID:24696800

  2. Development and Validation of a Heart Atlas to Study Cardiac Exposure to Radiation Following Treatment for Breast Cancer

    International Nuclear Information System (INIS)

    Feng, Mary; Moran, Jean M.; Koelling, Todd; Chughtai, Aamer; Chan, June L.; Freedman, Laura; Hayman, James A.; Jagsi, Reshma; Jolly, Shruti; Larouere, Janice; Soriano, Julie; Marsh, Robin; Pierce, Lori J.

    2011-01-01

    Purpose: Cardiac toxicity is an important sequela of breast radiotherapy. However, the relationship between dose to cardiac structures and subsequent toxicity has not been well defined, partially due to variations in substructure delineation, which can lead to inconsistent dose reporting and the failure to detect potential correlations. Here we have developed a heart atlas and evaluated its effect on contour accuracy and concordance. Methods and Materials: A detailed cardiac computed tomography scan atlas was developed jointly by cardiology, cardiac radiology, and radiation oncology. Seven radiation oncologists were recruited to delineate the whole heart, left main and left anterior descending interventricular branches, and right coronary arteries on four cases before and after studying the atlas. Contour accuracy was assessed by percent overlap with gold standard atlas volumes. The concordance index was also calculated. Standard radiation fields were applied. Doses to observer-contoured cardiac structures were calculated and compared with gold standard contour doses. Pre- and post-atlas values were analyzed using a paired t test. Results: The cardiac atlas significantly improved contour accuracy and concordance. Percent overlap and concordance index of observer-contoured cardiac and gold standard volumes were 2.3-fold improved for all structures (p < 0.002). After application of the atlas, reported mean doses to the whole heart, left main artery, left anterior descending interventricular branch, and right coronary artery were within 0.1, 0.9, 2.6, and 0.6 Gy, respectively, of gold standard doses. Conclusions: This validated University of Michigan cardiac atlas may serve as a useful tool in future studies assessing cardiac toxicity and in clinical trials which include dose volume constraints to the heart.

  3. Concordant Patterns of Brain Structure in Mothers with Recurrent Depression and Their Never-Depressed Daughters.

    Science.gov (United States)

    Foland-Ross, Lara C; Behzadian, Negin; LeMoult, Joelle; Gotlib, Ian H

    2016-01-01

    A growing body of research has demonstrated that having a mother with a history of major depressive disorder (MDD) is one of the strongest predictors of depression in adolescent offspring. Few studies, however, have assessed neural markers of this increased risk for depression, or examined whether risk-related anomalies in adolescents at maternal risk for depression are related to neural abnormalities in their depressed mothers. We addressed these questions by examining concordance in brain structure in two groups of participants: mothers with a history of depression and their never-depressed daughters, and never-depressed mothers and their never-depressed daughters. We scanned mothers with (remitted; RMD) and without (control; CTL) a history of recurrent episodes of depression and their never-depressed daughters, computed cortical gray matter thickness, and tested whether mothers' thickness predicted daughters' thickness. Both RMD mothers and their high-risk daughters exhibited focal areas of thinner cortical gray matter compared with their CTL/low-risk counterparts. Importantly, the extent of thickness anomalies in RMD mothers predicted analogous abnormalities in their daughters; this pattern was not present in CTL/low-risk dyads. We identified neuroanatomical risk factors that may underlie the intergenerational transmission of risk for MDD. Our findings suggest that there is concordance in brain structure in dyads that is affected by maternal depression, and that the location, direction, and extent of neural anomalies in high-risk offspring mirror those of their recurrent depressed mothers. © 2016 S. Karger AG, Basel.

  4. Automated brain structure segmentation based on atlas registration and appearance models

    DEFF Research Database (Denmark)

    van der Lijn, Fedde; de Bruijne, Marleen; Klein, Stefan

    2012-01-01

    Accurate automated brain structure segmentation methods facilitate the analysis of large-scale neuroimaging studies. This work describes a novel method for brain structure segmentation in magnetic resonance images that combines information about a structure’s location and appearance. The spatial...... with different magnetic resonance sequences, in which the hippocampus and cerebellum were segmented by an expert. Furthermore, the method is compared to two other segmentation techniques that were applied to the same data. Results show that the atlas- and appearance-based method produces accurate results...

  5. The INIA19 template and NeuroMaps atlas for primate brain image parcellation and spatial normalization

    Directory of Open Access Journals (Sweden)

    Torsten eRohlfing

    2012-12-01

    Full Text Available The INIA19 is a new, high-quality template for imaging-based studies of non-human primate brains created from high-resolution T1-weighted magnetic resonance (MR images of 19 rhesus macaque (Macaca mulatta animals. Combined with the comprehensive cortical and subcortical label map of the NeuroMaps atlas, the INIA19 is equally suitable for studies requiring both spatial normalization and atlas label propagation. Population-averaged template images are provided for both the brain and the whole head, to allow alignment of the atlas with both skull-stripped and unstripped data, and thus to facilitate its use for skull stripping of new images. This article describes the construction of the template using freely-available software tools, as well as the template itself, which is being made available to the scientific community (http://nitrc.org/projects/inia19/.

  6. The Brain of the Archerfish Toxotes chatareus: A Nissl-Based Neuroanatomical Atlas and Catecholaminergic/Cholinergic Systems

    Science.gov (United States)

    Karoubi, Naomi; Segev, Ronen; Wullimann, Mario F.

    2016-01-01

    Over recent years, the seven-spot archerfish (Toxotes chatareus) has emerged as a new model for studies in visual and behavioral neuroscience thanks to its unique hunting strategy. Its natural ability to spit at insects outside of water can be used in the laboratory for well controlled behavioral experiments where the fish is trained to aim at targets on a screen. The need for a documentation of the neuroanatomy of this animal became critical as more research groups use it as a model. Here we present an atlas of adult T. chatareus specimens caught in the wild in South East Asia. The atlas shows representative sections of the brain and specific structures revealed by a classic Nissl staining as well as corresponding schematic drawings. Additional immunostainings for catecholaminergic and cholinergic systems were conducted to corroborate the identification of certain nuclei and the data of a whole brain scanner is available online. We describe the general features of the archerfish brain as well as its specificities, especially for the visual system and compare the neuroanatomy of the archerfish with other teleosts. This atlas of the archerfish brain shows all levels of the neuraxis and intends to provide a solid basis for further neuroscientific research on T. chatareus, in particular electrophysiological studies. PMID:27891081

  7. Multidimensional MRI-CT atlas of the naked mole-rat brain (Heterocephalus glaber).

    Science.gov (United States)

    Seki, Fumiko; Hikishima, Keigo; Nambu, Sanae; Okanoya, Kazuo; Okano, Hirotaka J; Sasaki, Erika; Miura, Kyoko; Okano, Hideyuki

    2013-01-01

    Naked mole-rats have a variety of distinctive features such as the organization of a hierarchical society (known as eusociality), extraordinary longevity, and cancer resistance; thus, it would be worthwhile investigating these animals in detail. One important task is the preparation of a brain atlas database that provide comprehensive information containing multidimensional data with various image contrasts, which can be achievable using a magnetic resonance imaging (MRI). Advanced MRI techniques such as diffusion tensor imaging (DTI), which generates high contrast images of fiber structures, can characterize unique morphological properties in addition to conventional MRI. To obtain high spatial resolution images, MR histology, DTI, and X-ray computed tomography were performed on the fixed adult brain. Skull and brain structures were segmented as well as reconstructed in stereotaxic coordinates. Data were also acquired for the neonatal brain to allow developmental changes to be observed. Moreover, in vivo imaging of naked mole-rats was established as an evaluation tool of live animals. The data obtained comprised three-dimensional (3D) images with high tissue contrast as well as stereotaxic coordinates. Developmental differences in the visual system were highlighted in particular by DTI. Although it was difficult to delineate optic nerves in the mature adult brain, parts of them could be distinguished in the immature neonatal brain. From observation of cortical thickness, possibility of high somatosensory system development replaced to the visual system was indicated. 3D visualization of brain structures in the atlas as well as the establishment of in vivo imaging would promote neuroimaging researches towards detection of novel characteristics of eusocial naked mole-rats.

  8. Toward defining deep brain stimulation targets in MNI space: A subcortical atlas based on multimodal MRI, histology and structural connectivity.

    Science.gov (United States)

    Ewert, Siobhan; Plettig, Philip; Li, Ningfei; Chakravarty, M Mallar; Collins, D Louis; Herrington, Todd M; Kühn, Andrea A; Horn, Andreas

    2018-04-15

    Three-dimensional atlases of subcortical brain structures are valuable tools to reference anatomy in neuroscience and neurology. For instance, they can be used to study the position and shape of the three most common deep brain stimulation (DBS) targets, the subthalamic nucleus (STN), internal part of the pallidum (GPi) and ventral intermediate nucleus of the thalamus (VIM) in spatial relationship to DBS electrodes. Here, we present a composite atlas based on manual segmentations of a multimodal high resolution brain template, histology and structural connectivity. In a first step, four key structures were defined on the template itself using a combination of multispectral image analysis and manual segmentation. Second, these structures were used as anchor points to coregister a detailed histological atlas into standard space. Results show that this approach significantly improved coregistration accuracy over previously published methods. Finally, a sub-segmentation of STN and GPi into functional zones was achieved based on structural connectivity. The result is a composite atlas that defines key nuclei on the template itself, fills the gaps between them using histology and further subdivides them using structural connectivity. We show that the atlas can be used to segment DBS targets in single subjects, yielding more accurate results compared to priorly published atlases. The atlas will be made publicly available and constitutes a resource to study DBS electrode localizations in combination with modern neuroimaging methods. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Influence of Signal Intensity Non-Uniformity on Brain Volumetry Using an Atlas-Based Method

    International Nuclear Information System (INIS)

    Takao, Hidemasa; Kunimatsu, Akira; Mori, Harushi

    2012-01-01

    Many studies have reported pre-processing effects for brain volumetry; however, no study has investigated whether non-parametric non-uniform intensity normalization (N3) correction processing results in reduced system dependency when using an atlas-based method. To address this shortcoming, the present study assessed whether N3 correction processing provides reduced system dependency in atlas-based volumetry. Contiguous sagittal T1-weighted images of the brain were obtained from 21 healthy participants, by using five magnetic resonance protocols. After image preprocessing using the Statistical Parametric Mapping 5 software, we measured the structural volume of the segmented images with the WFU-PickAtlas software. We applied six different bias-correction levels (Regularization 10, Regularization 0.0001, Regularization 0, Regularization 10 with N3, Regularization 0.0001 with N3, and Regularization 0 with N3) to each set of images. The structural volume change ratio (%) was defined as the change ratio (%) = (100 X[measured volume - mean volume of five magnetic resonance protocols] / mean volume of five magnetic resonance protocols) for each bias-correction level. A low change ratio was synonymous with lower system dependency. The results showed that the images with the N3 correction had a lower change ratio compared with those without the N3 correction. The present study is the first atlas-based volumetry study to show that the precision of atlas-based volumetry improves when using N3-corrected images. Therefore, correction for signal intensity non-uniformity is strongly advised for multi-scanner or multi-site imaging trials.

  10. Influence of signal intensity non-uniformity on brain volumetry using an atlas-based method.

    Science.gov (United States)

    Goto, Masami; Abe, Osamu; Miyati, Tosiaki; Kabasawa, Hiroyuki; Takao, Hidemasa; Hayashi, Naoto; Kurosu, Tomomi; Iwatsubo, Takeshi; Yamashita, Fumio; Matsuda, Hiroshi; Mori, Harushi; Kunimatsu, Akira; Aoki, Shigeki; Ino, Kenji; Yano, Keiichi; Ohtomo, Kuni

    2012-01-01

    Many studies have reported pre-processing effects for brain volumetry; however, no study has investigated whether non-parametric non-uniform intensity normalization (N3) correction processing results in reduced system dependency when using an atlas-based method. To address this shortcoming, the present study assessed whether N3 correction processing provides reduced system dependency in atlas-based volumetry. Contiguous sagittal T1-weighted images of the brain were obtained from 21 healthy participants, by using five magnetic resonance protocols. After image preprocessing using the Statistical Parametric Mapping 5 software, we measured the structural volume of the segmented images with the WFU-PickAtlas software. We applied six different bias-correction levels (Regularization 10, Regularization 0.0001, Regularization 0, Regularization 10 with N3, Regularization 0.0001 with N3, and Regularization 0 with N3) to each set of images. The structural volume change ratio (%) was defined as the change ratio (%) = (100 × [measured volume - mean volume of five magnetic resonance protocols] / mean volume of five magnetic resonance protocols) for each bias-correction level. A low change ratio was synonymous with lower system dependency. The results showed that the images with the N3 correction had a lower change ratio compared with those without the N3 correction. The present study is the first atlas-based volumetry study to show that the precision of atlas-based volumetry improves when using N3-corrected images. Therefore, correction for signal intensity non-uniformity is strongly advised for multi-scanner or multi-site imaging trials.

  11. Influence of Signal Intensity Non-Uniformity on Brain Volumetry Using an Atlas-Based Method

    Energy Technology Data Exchange (ETDEWEB)

    Takao, Hidemasa; Kunimatsu, Akira; Mori, Harushi [University of Tokyo Hospital, Tokyo (Japan); and others

    2012-07-15

    Many studies have reported pre-processing effects for brain volumetry; however, no study has investigated whether non-parametric non-uniform intensity normalization (N3) correction processing results in reduced system dependency when using an atlas-based method. To address this shortcoming, the present study assessed whether N3 correction processing provides reduced system dependency in atlas-based volumetry. Contiguous sagittal T1-weighted images of the brain were obtained from 21 healthy participants, by using five magnetic resonance protocols. After image preprocessing using the Statistical Parametric Mapping 5 software, we measured the structural volume of the segmented images with the WFU-PickAtlas software. We applied six different bias-correction levels (Regularization 10, Regularization 0.0001, Regularization 0, Regularization 10 with N3, Regularization 0.0001 with N3, and Regularization 0 with N3) to each set of images. The structural volume change ratio (%) was defined as the change ratio (%) = (100 X[measured volume - mean volume of five magnetic resonance protocols] / mean volume of five magnetic resonance protocols) for each bias-correction level. A low change ratio was synonymous with lower system dependency. The results showed that the images with the N3 correction had a lower change ratio compared with those without the N3 correction. The present study is the first atlas-based volumetry study to show that the precision of atlas-based volumetry improves when using N3-corrected images. Therefore, correction for signal intensity non-uniformity is strongly advised for multi-scanner or multi-site imaging trials.

  12. Computation of an MRI brain atlas from a population of Parkinson’s disease patients

    Science.gov (United States)

    Angelidakis, L.; Papageorgiou, I. E.; Damianou, C.; Psychogios, M. N.; Lingor, P.; von Eckardstein, K.; Hadjidemetriou, S.

    2017-11-01

    Parkinson’s Disease (PD) is a degenerative disorder of the brain. This study presents an MRI-based brain atlas of PD to characterize associated alterations for diagnostic and interventional purposes. The atlas standardizes primarily the implicated subcortical regions such as the globus pallidus (GP), substantia nigra (SN), subthalamic nucleus (STN), caudate nucleus (CN), thalamus (TH), putamen (PUT), and red nucleus (RN). The data were 3.0 T MRI brain images from 16 PD patients and 10 matched controls. The images used were T1-weighted (T 1 w), T2-weighted (T 2 w) images, and Susceptibility Weighted Images (SWI). The T1w images were the reference for the inter-subject non-rigid registration available from 3DSlicer. Anatomic labeling was achieved with BrainSuite and regions were refined with the level sets segmentation of ITK-Snap. The subcortical centers were analyzed for their volume and signal intensity. Comparison with an age-matched control group unravels a significant PD-related T1w signal loss in the striatum (CN and PUT) centers, but approximately a constant volume. The results in this study improve MRI based PD localization and can lead to the development of novel biomarkers.

  13. A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus.

    Science.gov (United States)

    Simões, José M; Teles, Magda C; Oliveira, Rui F; Van der Linden, Annemie; Verhoye, Marleen

    2012-01-01

    The African cichlid Oreochromis mossambicus (Mozambique tilapia) has been used as a model system in a wide range of behavioural and neurobiological studies. The increasing number of genetic tools available for this species, together with the emerging interest in its use for neurobiological studies, increased the need for an accurate hodological mapping of the tilapia brain to supplement the available histological data. The goal of our study was to elaborate a three-dimensional, high-resolution digital atlas using magnetic resonance imaging, supported by Nissl staining. Resulting images were viewed and analysed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. This high resolution tilapia brain atlas is expected to become a very useful tool for neuroscientists using this fish model and will certainly expand their use in future studies regarding the central nervous system.

  14. A three-dimensional stereotaxic atlas of the gray short-tailed opossum (Monodelphis domestica) brain.

    Science.gov (United States)

    Majka, Piotr; Chlodzinska, Natalia; Turlejski, Krzysztof; Banasik, Tomasz; Djavadian, Ruzanna L; Węglarz, Władysław P; Wójcik, Daniel K

    2018-05-01

    The gray short-tailed opossum (Monodelphis domestica) is a small marsupial gaining recognition as a laboratory animal in biomedical research. Despite numerous studies on opossum neuroanatomy, a consistent and comprehensive neuroanatomical reference for this species is still missing. Here we present the first three-dimensional, multimodal atlas of the Monodelphis opossum brain. It is based on four complementary imaging modalities: high resolution ex vivo magnetic resonance images, micro-computed tomography scans of the cranium, images of the face of the cutting block, and series of sections stained with the Nissl method and for myelinated fibers. Individual imaging modalities were reconstructed into a three-dimensional form and then registered to the MR image by means of affine and deformable registration routines. Based on a superimposition of the 3D images, 113 anatomical structures were demarcated and the volumes of individual regions were measured. The stereotaxic coordinate system was defined using a set of cranial landmarks: interaural line, bregma, and lambda, which allows for easy expression of any location within the brain with respect to the skull. The atlas is released under the Creative Commons license and available through various digital atlasing web services.

  15. A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting

    International Nuclear Information System (INIS)

    Purger, David; McNutt, Todd; Wong, John; Ford, Eric; Achanta, Pragathi; Quinones-Hinojosa, Alfredo

    2009-01-01

    The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas' accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlases represent an accurate method to obtain accurate morphometric measurements of a population of mice, and that this method may be applied to phenotyping experiments in the future as well as precision targeting of surgical procedures or radiation treatment.

  16. A histology-based atlas of the C57BL/6J mouse brain deformably registered to in vivo MRI for localized radiation and surgical targeting

    Science.gov (United States)

    Purger, David; McNutt, Todd; Achanta, Pragathi; Quiñones-Hinojosa, Alfredo; Wong, John; Ford, Eric

    2009-12-01

    The C57BL/6J laboratory mouse is commonly used in neurobiological research. Digital atlases of the C57BL/6J brain have been used for visualization, genetic phenotyping and morphometry, but currently lack the ability to accurately calculate deviations between individual mice. We developed a fully three-dimensional digital atlas of the C57BL/6J brain based on the histology atlas of Paxinos and Franklin (2001 The Mouse Brain in Stereotaxic Coordinates 2nd edn (San Diego, CA: Academic)). The atlas uses triangular meshes to represent the various structures. The atlas structures can be overlaid and deformed to individual mouse MR images. For this study, we selected 18 structures from the histological atlas. Average atlases can be created for any group of mice of interest by calculating the mean three-dimensional positions of corresponding individual mesh vertices. As a validation of the atlas' accuracy, we performed deformable registration of the lateral ventricles to 13 MR brain scans of mice in three age groups: 5, 8 and 9 weeks old. Lateral ventricle structures from individual mice were compared to the corresponding average structures and the original histology structures. We found that the average structures created using our method more accurately represent individual anatomy than histology-based atlases alone, with mean vertex deviations of 0.044 mm versus 0.082 mm for the left lateral ventricle and 0.045 mm versus 0.068 mm for the right lateral ventricle. Our atlas representation gives direct spatial deviations for structures of interest. Our results indicate that MR-deformable histology-based atlases represent an accurate method to obtain accurate morphometric measurements of a population of mice, and that this method may be applied to phenotyping experiments in the future as well as precision targeting of surgical procedures or radiation treatment.

  17. Specifying the brain anatomy underlying temporo-parietal junction activations for theory of mind: A review using probabilistic atlases from different imaging modalities.

    Science.gov (United States)

    Schurz, Matthias; Tholen, Matthias G; Perner, Josef; Mars, Rogier B; Sallet, Jerome

    2017-09-01

    In this quantitative review, we specified the anatomical basis of brain activity reported in the Temporo-Parietal Junction (TPJ) in Theory of Mind (ToM) research. Using probabilistic brain atlases, we labeled TPJ peak coordinates reported in the literature. This was carried out for four different atlas modalities: (i) gyral-parcellation, (ii) sulco-gyral parcellation, (iii) cytoarchitectonic parcellation and (iv) connectivity-based parcellation. In addition, our review distinguished between two ToM task types (false belief and social animations) and a nonsocial task (attention reorienting). We estimated the mean probabilities of activation for each atlas label, and found that for all three task types part of TPJ activations fell into the same areas: (i) Angular Gyrus (AG) and Lateral Occpital Cortex (LOC) in terms of a gyral atlas, (ii) AG and Superior Temporal Sulcus (STS) in terms of a sulco-gyral atlas, (iii) areas PGa and PGp in terms of cytoarchitecture and (iv) area TPJp in terms of a connectivity-based parcellation atlas. Beside these commonalities, we also found that individual task types showed preferential activation for particular labels. Main findings for the right hemisphere were preferential activation for false belief tasks in AG/PGa, and in Supramarginal Gyrus (SMG)/PFm for attention reorienting. Social animations showed strongest selective activation in the left hemisphere, specifically in left Middle Temporal Gyrus (MTG). We discuss how our results (i.e., identified atlas structures) can provide a new reference for describing future findings, with the aim to integrate different labels and terminologies used for studying brain activity around the TPJ. Hum Brain Mapp 38:4788-4805, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps

    Science.gov (United States)

    2018-01-01

    Abstract The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to “Google Maps” for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3‐D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. PMID:29277900

  19. Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps.

    Science.gov (United States)

    Swanson, Larry W

    2018-04-15

    The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry. A second new feature is an aligned atlas of bilateral flatmaps illustrating rat nervous system development from the neural plate stage to the adult stage, where most gray matter regions, white matter tracts, ganglia, and nerves listed in the nomenclature tables are illustrated schematically. These flatmaps are convenient for future development of online applications analogous to "Google Maps" for systems neuroscience. The third new feature is a completely revised Atlas of the rat brain in spatially aligned transverse sections that can serve as a framework for 3-D modeling. Atlas parcellation is little changed from the preceding edition, but the nomenclature for rat is now aligned with an emerging panmammalian neuroanatomical nomenclature. All figures are presented in Adobe Illustrator vector graphics format that can be manipulated, modified, and resized as desired, and freely used with a Creative Commons license. © 2018 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

  20. Concorde

    CERN Multimedia

    Bernard

    1971-01-01

    Concorde -volera, volera pas et comment volera-t-il? Film: les Concordes de vol Le Commandant Bernard présente le Concorde, "né" en 1962, et commente l'appareil qui est d'actualité- commentaires techniques à l'aide d'une maquette et présentation des dias

  1. Towards an elastographic atlas of brain anatomy.

    Directory of Open Access Journals (Sweden)

    Jing Guo

    Full Text Available Cerebral viscoelastic constants can be measured in a noninvasive, image-based way by magnetic resonance elastography (MRE for the detection of neurological disorders. However, MRE brain maps of viscoelastic constants are still limited by low spatial resolution. Here we introduce three-dimensional multifrequency MRE of the brain combined with a novel reconstruction algorithm based on a model-free multifrequency inversion for calculating spatially resolved viscoelastic parameter maps of the human brain corresponding to the dynamic range of shear oscillations between 30 and 60 Hz. Maps of two viscoelastic parameters, the magnitude and the phase angle of the complex shear modulus, |G*| and φ, were obtained and normalized to group templates of 23 healthy volunteers in the age range of 22 to 72 years. This atlas of the anatomy of brain mechanics reveals a significant contrast in the stiffness parameter |G*| between different anatomical regions such as white matter (WM; 1.252±0.260 kPa, the corpus callosum genu (CCG; 1.104±0.280 kPa, the thalamus (TH; 1.058±0.208 kPa and the head of the caudate nucleus (HCN; 0.649±0.101 kPa. φ, which is sensitive to the lossy behavior of the tissue, was in the order of CCG (1.011±0.172, TH (1.037±0.173, CN (0.906±0.257 and WM (0.854±0.169. The proposed method provides the first normalized maps of brain viscoelasticity with anatomical details in subcortical regions and provides useful background data for clinical applications of cerebral MRE.

  2. 75 FR 69470 - Tele Atlas North America, Inc., Currently Doing Business as Tom Tom Including Off-Site Workers...

    Science.gov (United States)

    2010-11-12

    ...,839B; TA-W-70,839C] Tele Atlas North America, Inc., Currently Doing Business as Tom Tom Including Off... Business as Tom Tom, Concord, MA; Tele Atlas North America, Inc. Currently Doing Business as Tom Tom, Detroit, MI; Tele Atlas North America, Inc. Currently Doing Business as Tom Tom, Redwood, CA; Amended...

  3. Automatic registration of imaging mass spectrometry data to the Allen Brain Atlas transcriptome

    Science.gov (United States)

    Abdelmoula, Walid M.; Carreira, Ricardo J.; Shyti, Reinald; Balluff, Benjamin; Tolner, Else; van den Maagdenberg, Arn M. J. M.; Lelieveldt, B. P. F.; McDonnell, Liam; Dijkstra, Jouke

    2014-03-01

    Imaging Mass Spectrometry (IMS) is an emerging molecular imaging technology that provides spatially resolved information on biomolecular structures; each image pixel effectively represents a molecular mass spectrum. By combining the histological images and IMS-images, neuroanatomical structures can be distinguished based on their biomolecular features as opposed to morphological features. The combination of IMS data with spatially resolved gene expression maps of the mouse brain, as provided by the Allen Mouse Brain atlas, would enable comparative studies of spatial metabolic and gene expression patterns in life-sciences research and biomarker discovery. As such, it would be highly desirable to spatially register IMS slices to the Allen Brain Atlas (ABA). In this paper, we propose a multi-step automatic registration pipeline to register ABA histology to IMS- images. Key novelty of the method is the selection of the best reference section from the ABA, based on pre-processed histology sections. First, we extracted a hippocampus-specific geometrical feature from the given experimental histological section to initially localize it among the ABA sections. Then, feature-based linear registration is applied to the initially localized section and its two neighbors in the ABA to select the most similar reference section. A non-rigid registration yields a one-to-one mapping of the experimental IMS slice to the ABA. The pipeline was applied on 6 coronal sections from two mouse brains, showing high anatomical correspondence, demonstrating the feasibility of complementing biomolecule distributions from individual mice with the genome-wide ABA transcriptome.

  4. Regional growth and atlasing of the developing human brain.

    Science.gov (United States)

    Makropoulos, Antonios; Aljabar, Paul; Wright, Robert; Hüning, Britta; Merchant, Nazakat; Arichi, Tomoki; Tusor, Nora; Hajnal, Joseph V; Edwards, A David; Counsell, Serena J; Rueckert, Daniel

    2016-01-15

    Detailed morphometric analysis of the neonatal brain is required to characterise brain development and define neuroimaging biomarkers related to impaired brain growth. Accurate automatic segmentation of neonatal brain MRI is a prerequisite to analyse large datasets. We have previously presented an accurate and robust automatic segmentation technique for parcellating the neonatal brain into multiple cortical and subcortical regions. In this study, we further extend our segmentation method to detect cortical sulci and provide a detailed delineation of the cortical ribbon. These detailed segmentations are used to build a 4-dimensional spatio-temporal structural atlas of the brain for 82 cortical and subcortical structures throughout this developmental period. We employ the algorithm to segment an extensive database of 420 MR images of the developing brain, from 27 to 45weeks post-menstrual age at imaging. Regional volumetric and cortical surface measurements are derived and used to investigate brain growth and development during this critical period and to assess the impact of immaturity at birth. Whole brain volume, the absolute volume of all structures studied, cortical curvature and cortical surface area increased with increasing age at scan. Relative volumes of cortical grey matter, cerebellum and cerebrospinal fluid increased with age at scan, while relative volumes of white matter, ventricles, brainstem and basal ganglia and thalami decreased. Preterm infants at term had smaller whole brain volumes, reduced regional white matter and cortical and subcortical grey matter volumes, and reduced cortical surface area compared with term born controls, while ventricular volume was greater in the preterm group. Increasing prematurity at birth was associated with a reduction in total and regional white matter, cortical and subcortical grey matter volume, an increase in ventricular volume, and reduced cortical surface area. Copyright © 2015 The Authors. Published by

  5. Multiscale Exploration of Mouse Brain Microstructures Using the Knife-Edge Scanning Microscope Brain Atlas

    Directory of Open Access Journals (Sweden)

    Ji Ryang Chung

    2011-11-01

    Full Text Available Connectomics is the study of the full connection matrix of the brain.Recent advances in high-throughput, high-resolution 3D microscopy methodshave enabled the imaging of whole small animal brains at a sub-micrometerresolution, potentially opening the road to full-blown connectomicsresearch. One of the first such instruments to achieve whole-brain-scaleimaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope(KESM. KESM whole-brain data sets now include Golgi (neuronal circuits,Nissl (soma distribution, and India ink (vascular networks. KESM data cancontribute greatly to connectomics research, since they fill the gap betweenlower resolution, large volume imaging methods (such as diffusion MRI andhigher resolution, small volume methods (e.g., serial sectioning electronmicroscopy. Furthermore, KESM data are by their nature multiscale, ranging fromthe subcellular to the whole organ scale. Due to this, visualization alone is ahuge challenge, before we even start worrying about connectivity analysis. Tosolve this issue, we developed a web-based neuroinformatics framework for efficientvisualization and analysis of the multiscale KESM data sets. In this paper,we will first provide an overview of KESM, then discuss in detail the KESMdata sets and the web-based neuroinformatics framework, which is called theKESM Brain Atlas (KESMBA. Finally, we will discuss the relevance of the KESMBAto connectomics research, and identify challenges and future directions.

  6. Automatic Testing and Assessment of Neuroanatomy Using a Digital Brain Atlas: Method and Development of Computer- and Mobile-Based Applications

    Science.gov (United States)

    Nowinski, Wieslaw L.; Thirunavuukarasuu, Arumugam; Ananthasubramaniam, Anand; Chua, Beng Choon; Qian, Guoyu; Nowinska, Natalia G.; Marchenko, Yevgen; Volkau, Ihar

    2009-01-01

    Preparation of tests and student's assessment by the instructor are time consuming. We address these two tasks in neuroanatomy education by employing a digital media application with a three-dimensional (3D), interactive, fully segmented, and labeled brain atlas. The anatomical and vascular models in the atlas are linked to "Terminologia…

  7. Concordance between brain 18F-FDG PET and cerebrospinal fluid biomarkers in diagnosing Alzheimer's disease.

    Science.gov (United States)

    Rubí, S; Noguera, A; Tarongí, S; Oporto, M; García, A; Vico, H; Espino, A; Picado, M J; Mas, A; Peña, C; Amer, G

    Cortical posterior hypometabolism on PET imaging with 18 F-FDG (FDG-PET), and altered levels of Aß 1-42 peptide, total Tau (tTau) and phosphorylated Tau (pTau) proteins in cerebrospinal fluid (CSF) are established diagnostic biomarkers in Alzheimer's disease (AD). An evaluation has been made of the concordance and relationship between the results of FDG-PET and CSF biomarkers in symptomatic patients with suspected AD. A retrospective review was carried out on 120 patients with cognitive impairment referred to our Cognitive Neurology Unit, and who were evaluated by brain FDG-PET and a lumbar puncture for CSF biomarkers. In order to calculate their Kappa coefficient of concordance, the result of the FDG-PET and the set of the three CSF biomarkers in each patient was classified as normal, inconclusive, or AD-compatible. The relationship between the results of both methods was further assessed using logistic regression analysis, including the Aß 1-42 , tTau and pTau levels as quantitative predictors, and the FDG-PET result as the dependent variable. The weighted Kappa coefficient between FDG-PET and CSF biomarkers was 0.46 (95% CI: 0.35-0.57). Logistic regression analysis showed that the Aß 1-42 and tTau values together were capable of discriminating an FDG-PET result metabolically suggestive of AD from one non-suggestive of AD, with a 91% sensitivity and 93% specificity at the cut-off line Aß 1-42 =44+1.3×tTau. The level of concordance between FDG-PET and CSF biomarkers was moderate, indicating their complementary value in diagnosing AD. The Aß 1-42 and tTau levels in CSF help to predict the patient FDG-PET cortical metabolic status. Copyright © 2017 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

  8. Automated delineation of brain structures in patients undergoing radiotherapy for primary brain tumors: From atlas to dose–volume histograms

    International Nuclear Information System (INIS)

    Conson, Manuel; Cella, Laura; Pacelli, Roberto; Comerci, Marco; Liuzzi, Raffaele; Salvatore, Marco; Quarantelli, Mario

    2014-01-01

    Purpose: To implement and evaluate a magnetic resonance imaging atlas-based automated segmentation (MRI-ABAS) procedure for cortical and sub-cortical grey matter areas definition, suitable for dose-distribution analyses in brain tumor patients undergoing radiotherapy (RT). Patients and methods: 3T-MRI scans performed before RT in ten brain tumor patients were used. The MRI-ABAS procedure consists of grey matter classification and atlas-based regions of interest definition. The Simultaneous Truth and Performance Level Estimation (STAPLE) algorithm was applied to structures manually delineated by four experts to generate the standard reference. Performance was assessed comparing multiple geometrical metrics (including Dice Similarity Coefficient – DSC). Dosimetric parameters from dose–volume-histograms were also generated and compared. Results: Compared with manual delineation, MRI-ABAS showed excellent reproducibility [median DSC ABAS = 1 (95% CI, 0.97–1.0) vs. DSC MANUAL = 0.90 (0.73–0.98)], acceptable accuracy [DSC ABAS = 0.81 (0.68–0.94) vs. DSC MANUAL = 0.90 (0.76–0.98)], and an overall 90% reduction in delineation time. Dosimetric parameters obtained using MRI-ABAS were comparable with those obtained by manual contouring. Conclusions: The speed, reproducibility, and robustness of the process make MRI-ABAS a valuable tool for investigating radiation dose–volume effects in non-target brain structures providing additional standardized data without additional time-consuming procedures

  9. A digital interactive human brain atlas based on Chinese visible human datasets for anatomy teaching.

    Science.gov (United States)

    Li, Qiyu; Ran, Xu; Zhang, Shaoxiang; Tan, Liwen; Qiu, Mingguo

    2014-01-01

    As we know, the human brain is one of the most complicated organs in the human body, which is the key and difficult point in neuroanatomy and sectional anatomy teaching. With the rapid development and extensive application of imaging technology in clinical diagnosis, doctors are facing higher and higher requirement on their anatomy knowledge. Thus, to cultivate medical students to meet the needs of medical development today and to improve their ability to read and understand radiographic images have become urgent challenges for the medical teachers. In this context, we developed a digital interactive human brain atlas based on the Chinese visible human datasets for anatomy teaching (available for free download from http://www.chinesevisiblehuman.com/down/DHBA.rar). The atlas simultaneously provides views in all 3 primary planes of section. The main structures of the human brain have been anatomically labeled in all 3 views. It is potentially useful for anatomy browsing, user self-testing, and automatic student assessment. In a word, it is interactive, 3D, user friendly, and free of charge, which can provide a new, intuitive means for anatomy teaching.

  10. The Cerefy Atlas of brain anatomy. An interactive reference tool for students, teachers and researchers

    International Nuclear Information System (INIS)

    Nowinski, W.L.; Thirunavuukarasuu, A.; Bryan, R.N.

    2002-01-01

    The Cerefy registered Atlas of Brain Anatomy is a remarkable accomplishment combining the best of current neuroanatomical methodology with the amazing capability of the modern personal computer. This CD-ROM not only demonstrates the power of digital technology, but also provides a view of the future of medical education. Through the use of magnetic resonance images (MRI) combined with interactive image labeling it is possible to use this CD-ROM to rapidly name any structure within the brain in three planes of section presented simultaneously. With the simple click of a mouse of most intricate of brain structures can be identified in sagittal, axial, and coronal planes. By selecting the ''label'' function, whatever brain structure the cursor is placed upon is named in real time. It is possible to literally browse across the brain and watch every structure that is touched be named on the screen as fast as you can move the cursor. This incredible functionality is further enhanced by the ability to select the test mode and provide a self-guided quiz of neuroanatomy. This atlas is perfect for preparing teaching materials as it also contains a ''save'' function to preserve labeled images. This low-cost CD-ROM will no doubt be used by those who study and/or teach neuroanatomy, neurology, neurosurgery, neuroradiology, neuroscience, neuropsychology, and psychiatry. This unique contribution to the field of neuroanatomy is a most impressive accomplishment. (orig.)

  11. The Cerefy Atlas of brain anatomy. An interactive reference tool for students, teachers and researchers

    Energy Technology Data Exchange (ETDEWEB)

    Nowinski, W.L.; Thirunavuukarasuu, A.; Bryan, R.N.

    2002-07-01

    The Cerefy {sup registered} Atlas of Brain Anatomy is a remarkable accomplishment combining the best of current neuroanatomical methodology with the amazing capability of the modern personal computer. This CD-ROM not only demonstrates the power of digital technology, but also provides a view of the future of medical education. Through the use of magnetic resonance images (MRI) combined with interactive image labeling it is possible to use this CD-ROM to rapidly name any structure within the brain in three planes of section presented simultaneously. With the simple click of a mouse of most intricate of brain structures can be identified in sagittal, axial, and coronal planes. By selecting the ''label'' function, whatever brain structure the cursor is placed upon is named in real time. It is possible to literally browse across the brain and watch every structure that is touched be named on the screen as fast as you can move the cursor. This incredible functionality is further enhanced by the ability to select the test mode and provide a self-guided quiz of neuroanatomy. This atlas is perfect for preparing teaching materials as it also contains a ''save'' function to preserve labeled images. This low-cost CD-ROM will no doubt be used by those who study and/or teach neuroanatomy, neurology, neurosurgery, neuroradiology, neuroscience, neuropsychology, and psychiatry. This unique contribution to the field of neuroanatomy is a most impressive accomplishment. (orig.)

  12. Technical and organizational considerations for the long-term maintenance and development of digital brain atlases and web-based databases.

    Science.gov (United States)

    Ito, Kei

    2010-01-01

    Digital brain atlas is a kind of image database that specifically provide information about neurons and glial cells in the brain. It has various advantages that are unmatched by conventional paper-based atlases. Such advantages, however, may become disadvantages if appropriate cares are not taken. Because digital atlases can provide unlimited amount of data, they should be designed to minimize redundancy and keep consistency of the records that may be added incrementally by different staffs. The fact that digital atlases can easily be revised necessitates a system to assure that users can access previous versions that might have been cited in papers at a particular period. To inherit our knowledge to our descendants, such databases should be maintained for a very long period, well over 100 years, like printed books and papers. Technical and organizational measures to enable long-term archive should be considered seriously. Compared to the initial development of the database, subsequent efforts to increase the quality and quantity of its contents are not regarded highly, because such tasks do not materialize in the form of publications. This fact strongly discourages continuous expansion of, and external contributions to, the digital atlases after its initial launch. To solve these problems, the role of the biocurators is vital. Appreciation of the scientific achievements of the people who do not write papers, and establishment of the secure academic career path for them, are indispensable for recruiting talents for this very important job.

  13. A digital atlas to characterize the mouse brain transcriptome.

    Directory of Open Access Journals (Sweden)

    James P Carson

    2005-09-01

    Full Text Available Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer IV somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities.

  14. A review of Edward Flatau's 1894 Atlas of the Human Brain by the neurologist Sigmund Freud.

    Science.gov (United States)

    Triarhou, Lazaros C

    2011-01-01

    In 1894, the Polish neurologist Edward Flatau (1868-1932), working in Berlin, published an exquisite photographic atlas of the unfixed human brain, preceding by 2 years Das Menschenhirn, the reference work of Gustaf Retzius (1842-1919) in Stockholm. In his early career as a neuroanatomist and neurologist, Sigmund Freud (1856-1939) wrote a review of Flatau's atlas for the Internationale klinische Rundschau, which has not been included in the 'Standard Edition of the Complete Psychological Works'. The aim of the present paper is twofold: to document Freud's review, and to revive the largely forgotten atlas of Flatau. The full text of Freud is presented in translation. Further, one element Flatau, Retzius and Freud had in common is discussed: their early role as protagonists and firm supporters of Ramón y Cajal's neuron theory, the cornerstone of modern neuroscience. Copyright © 2010 S. Karger AG, Basel.

  15. The study of automatic brain extraction of basal ganglia based on atlas of Talairach in 18F-FDG PET images

    International Nuclear Information System (INIS)

    Zuo Chantao; Guan Yihui; Zhao Jun; Lin Xiangtong; Wang Jian; Zhang Jiange; Zhang Lu

    2005-01-01

    Objective: To establish a method which can extract functional areas of the brain basal ganglia automatically. Methods: 18 F-fluorodeoxyglucose (FDG) PET images were spatial normalized to Talairach atlas space through two steps, image registration and image deformation. The functional areas were extracted from three dimension PET images based on the coordinate obtained from atlas; caudate and putamen were extracted and rendered, the grey value of the area was normalized by whole brain. Results: The normal ratio of left caudate head, body and tail were 1.02 ± 0.04, 0.92 ± 0.07 and 0.71 ± 0.03, the right were 0.98 ± 0.03, 0.87 ± 0.04 and 0.71 ± 0.01 respectively. The normal ratio of left and right putamen were 1.20 ± 0.06 and 1.20 ± 0.04. The mean grey value between left and right basal ganglia had no significant difference (P>0.05). Conclusion: The automatic functional area extracting method based on atlas of Talairach is feasible. (authors)

  16. Specifying the brain anatomy underlying temporo-parietal junction activations for theory of mind: A review using probabilistic atlases from different imaging modalities

    NARCIS (Netherlands)

    Schurz, M.; Tholen, M.G.; Perner, J.; Mars, R.B.; Sallet, J.

    2017-01-01

    In this quantitative review, we specified the anatomical basis of brain activity reported in the Temporo-Parietal Junction (TPJ) in Theory of Mind (ToM) research. Using probabilistic brain atlases, we labeled TPJ peak coordinates reported in the literature. This was carried out for four different

  17. Know your tools - concordance of different methods for measuring brain volume change after ischemic stroke

    Energy Technology Data Exchange (ETDEWEB)

    Yassi, Nawaf; Campbell, Bruce C.V.; Davis, Stephen M.; Bivard, Andrew [The University of Melbourne, Departments of Medicine and Neurology, Melbourne Brain Centre rate at The Royal Melbourne Hospital, Parkville, Victoria (Australia); Moffat, Bradford A.; Steward, Christopher; Desmond, Patricia M. [The University of Melbourne, Department of Radiology, The Royal Melbourne Hospital, Parkville (Australia); Churilov, Leonid [The University of Melbourne, The Florey Institute of Neurosciences and Mental Health, Parkville (Australia); Parsons, Mark W. [University of Newcastle and Hunter Medical Research Institute, Priority Research Centre for Translational Neuroscience and Mental Health, Newcastle (Australia)

    2015-07-15

    Longitudinal brain volume changes have been investigated in a number of cerebral disorders as a surrogate marker of clinical outcome. In stroke, unique methodological challenges are posed by dynamic structural changes occurring after onset, particularly those relating to the infarct lesion. We aimed to evaluate agreement between different analysis methods for the measurement of post-stroke brain volume change, and to explore technical challenges inherent to these methods. Fifteen patients with anterior circulation stroke underwent magnetic resonance imaging within 1 week of onset and at 1 and 3 months. Whole-brain as well as grey- and white-matter volume were estimated separately using both an intensity-based and a surface watershed-based algorithm. In the case of the intensity-based algorithm, the analysis was also performed with and without exclusion of the infarct lesion. Due to the effects of peri-infarct edema at the baseline scan, longitudinal volume change was measured as percentage change between the 1 and 3-month scans. Intra-class and concordance correlation coefficients were used to assess agreement between the different analysis methods. Reduced major axis regression was used to inspect the nature of bias between measurements. Overall agreement between methods was modest with strong disagreement between some techniques. Measurements were variably impacted by procedures performed to account for infarct lesions. Improvements in volumetric methods and consensus between methodologies employed in different studies are necessary in order to increase the validity of conclusions derived from post-stroke cerebral volumetric studies. Readers should be aware of the potential impact of different methods on study conclusions. (orig.)

  18. Know your tools - concordance of different methods for measuring brain volume change after ischemic stroke

    International Nuclear Information System (INIS)

    Yassi, Nawaf; Campbell, Bruce C.V.; Davis, Stephen M.; Bivard, Andrew; Moffat, Bradford A.; Steward, Christopher; Desmond, Patricia M.; Churilov, Leonid; Parsons, Mark W.

    2015-01-01

    Longitudinal brain volume changes have been investigated in a number of cerebral disorders as a surrogate marker of clinical outcome. In stroke, unique methodological challenges are posed by dynamic structural changes occurring after onset, particularly those relating to the infarct lesion. We aimed to evaluate agreement between different analysis methods for the measurement of post-stroke brain volume change, and to explore technical challenges inherent to these methods. Fifteen patients with anterior circulation stroke underwent magnetic resonance imaging within 1 week of onset and at 1 and 3 months. Whole-brain as well as grey- and white-matter volume were estimated separately using both an intensity-based and a surface watershed-based algorithm. In the case of the intensity-based algorithm, the analysis was also performed with and without exclusion of the infarct lesion. Due to the effects of peri-infarct edema at the baseline scan, longitudinal volume change was measured as percentage change between the 1 and 3-month scans. Intra-class and concordance correlation coefficients were used to assess agreement between the different analysis methods. Reduced major axis regression was used to inspect the nature of bias between measurements. Overall agreement between methods was modest with strong disagreement between some techniques. Measurements were variably impacted by procedures performed to account for infarct lesions. Improvements in volumetric methods and consensus between methodologies employed in different studies are necessary in order to increase the validity of conclusions derived from post-stroke cerebral volumetric studies. Readers should be aware of the potential impact of different methods on study conclusions. (orig.)

  19. Quantitative Evaluation of Atlas-based Attenuation Correction for Brain PET in an Integrated Time-of-Flight PET/MR Imaging System.

    Science.gov (United States)

    Yang, Jaewon; Jian, Yiqiang; Jenkins, Nathaniel; Behr, Spencer C; Hope, Thomas A; Larson, Peder E Z; Vigneron, Daniel; Seo, Youngho

    2017-07-01

    Purpose To assess the patient-dependent accuracy of atlas-based attenuation correction (ATAC) for brain positron emission tomography (PET) in an integrated time-of-flight (TOF) PET/magnetic resonance (MR) imaging system. Materials and Methods Thirty recruited patients provided informed consent in this institutional review board-approved study. All patients underwent whole-body fluorodeoxyglucose PET/computed tomography (CT) followed by TOF PET/MR imaging. With use of TOF PET data, PET images were reconstructed with four different attenuation correction (AC) methods: PET with patient CT-based AC (CTAC), PET with ATAC (air and bone from an atlas), PET with ATAC patientBone (air and tissue from the atlas with patient bone), and PET with ATAC boneless (air and tissue from the atlas without bone). For quantitative evaluation, PET mean activity concentration values were measured in 14 1-mL volumes of interest (VOIs) distributed throughout the brain and statistical significance was tested with a paired t test. Results The mean overall difference (±standard deviation) of PET with ATAC compared with PET with CTAC was -0.69 kBq/mL ± 0.60 (-4.0% ± 3.2) (P PET with ATAC boneless (-9.4% ± 3.7) was significantly worse than that of PET with ATAC (-4.0% ± 3.2) (P PET with ATAC patientBone (-1.5% ± 1.5) improved over that of PET with ATAC (-4.0% ± 3.2) (P PET/MR imaging achieves similar quantification accuracy to that from CTAC by means of atlas-based bone compensation. However, patient-specific anatomic differences from the atlas causes bone attenuation differences and misclassified sinuses, which result in patient-dependent performance variation of ATAC. © RSNA, 2017 Online supplemental material is available for this article.

  20. FIIND: Ferret Interactive Integrated Neurodevelopment Atlas

    Directory of Open Access Journals (Sweden)

    Roberto Toro

    2018-03-01

    Full Text Available The first days after birth in ferrets provide a privileged view of the development of a complex mammalian brain. Unlike mice, ferrets develop a rich pattern of deep neocortical folds and cortico- cortical connections. Unlike humans and other primates, whose brains are well differentiated and folded at birth, ferrets are born with a very immature and completely smooth neocortex: folds, neocortical regionalisation and cortico-cortical connectivity develop in ferrets during the first postnatal days. After a period of fast neocortical expansion, during which brain volume increases by up to a factor of 4 in 2 weeks, the ferret brain reaches its adult volume at about 6 weeks of age. Ferrets could thus become a major animal model to investigate the neurobiological correlates of the phenomena observed in human neuroimaging. Many of these phenomena, such as the relationship between brain folding, cortico-cortical connectivity and neocortical regionalisation cannot be investigated in mice, but could be investigated in ferrets. Our aim is to provide the research community with a detailed description of the development of a complex brain, necessary to better understand the nature of human neuroimaging data, create models of brain development, or analyse the relationship between multiple spatial scales. We have already started a project to constitute an open, collaborative atlas of ferret brain development, integrating multi-modal and multi-scale data. We have acquired data for 28 ferrets (4 animals per time point from P0 to adults, using high-resolution MRI and diffusion tensor imaging (DTI. We have developed an open-source pipeline to segment and produce – online – 3D reconstructions of brain MRI data. We propose to process the brains of 16 of our specimens (from P0 to P16 using high-throughput 3D histology, staining for cytoarchitectonic landmarks, neuronal progenitors and neurogenesis. This would allow us to relate the MRI data that we have already

  1. Brain atlas for functional imaging. Clinical and research applications

    International Nuclear Information System (INIS)

    Nowinski, W.L.; Thirunavuukarasuu, A.; Kennedy, D.N

    2001-01-01

    This CD-ROM: Allows anatomical and functional images to be loaded and registered. Enables interactive placement of the Talairach landmarks in 3D Space. Provides automatic data-to-atlas warping based on the Talairaich proportional gridsystem transformation. Real-time interactive warping for fine tuning is also available. Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them in three planes. Mark placement is assisted by image thresholding. Provides simultaneous display of the atlas, anatomical image and functional image within one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann's areas and gyri can be labeled on both hemispheres. Provides additional functions such as friendly navigation, cross-referenced display, readout of the Talairach coordinates and intensities, load coordinates, save, on-line help. (orig.)

  2. Brain atlas for functional imaging. Clinical and research applications

    Energy Technology Data Exchange (ETDEWEB)

    Nowinski, W.L.; Thirunavuukarasuu, A.; Kennedy, D.N

    2001-07-01

    This CD-ROM: Allows anatomical and functional images to be loaded and registered. Enables interactive placement of the Talairach landmarks in 3D Space. Provides automatic data-to-atlas warping based on the Talairaich proportional gridsystem transformation. Real-time interactive warping for fine tuning is also available. Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them in three planes. Mark placement is assisted by image thresholding. Provides simultaneous display of the atlas, anatomical image and functional image within one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann's areas and gyri can be labeled on both hemispheres. Provides additional functions such as friendly navigation, cross-referenced display, readout of the Talairach coordinates and intensities, load coordinates, save, on-line help. (orig.)

  3. Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

    Science.gov (United States)

    Khan, Arshad M.; Perez, Jose G.; Wells, Claire E.; Fuentes, Olac

    2018-01-01

    The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including

  4. Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

    Directory of Open Access Journals (Sweden)

    Arshad M. Khan

    2018-05-01

    Full Text Available The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982 or Swanson (S, first published in 1992 as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z measured from the skull landmark, Bregma (β. Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT and Random Sample Consensus (RANSAC operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S

  5. The Stable Concordance Genus

    OpenAIRE

    Kearney, M. Kate

    2013-01-01

    The concordance genus of a knot is the least genus of any knot in its concordance class. Although difficult to compute, it is a useful invariant that highlights the distinction between the three-genus and four-genus. In this paper we define and discuss the stable concordance genus of a knot, which describes the behavior of the concordance genus under connected sum.

  6. Validating atlas-guided DOT: a comparison of diffuse optical tomography informed by atlas and subject-specific anatomies.

    Science.gov (United States)

    Cooper, Robert J; Caffini, Matteo; Dubb, Jay; Fang, Qianqian; Custo, Anna; Tsuzuki, Daisuke; Fischl, Bruce; Wells, William; Dan, Ippeita; Boas, David A

    2012-09-01

    We describe the validation of an anatomical brain atlas approach to the analysis of diffuse optical tomography (DOT). Using MRI data from 32 subjects, we compare the diffuse optical images of simulated cortical activation reconstructed using a registered atlas with those obtained using a subject's true anatomy. The error in localization of the simulated cortical activations when using a registered atlas is due to a combination of imperfect registration, anatomical differences between atlas and subject anatomies and the localization error associated with diffuse optical image reconstruction. When using a subject-specific MRI, any localization error is due to diffuse optical image reconstruction only. In this study we determine that using a registered anatomical brain atlas results in an average localization error of approximately 18 mm in Euclidean space. The corresponding error when the subject's own MRI is employed is 9.1 mm. In general, the cost of using atlas-guided DOT in place of subject-specific MRI-guided DOT is a doubling of the localization error. Our results show that despite this increase in error, reasonable anatomical localization is achievable even in cases where the subject-specific anatomy is unavailable. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. Exercises in Anatomy, Connectivity, and Morphology using Neuromorpho.org and the Allen Brain Atlas.

    Science.gov (United States)

    Chu, Philip; Peck, Joshua; Brumberg, Joshua C

    2015-01-01

    Laboratory instruction of neuroscience is often limited by the lack of physical resources and supplies (e.g., brains specimens, dissection kits, physiological equipment). Online databases can serve as supplements to material labs by providing professionally collected images of brain specimens and their underlying cellular populations with resolution and quality that is extremely difficult to access for strictly pedagogical purposes. We describe a method using two online databases, the Neuromorpho.org and the Allen Brain Atlas (ABA), that freely provide access to data from working brain scientists that can be modified for laboratory instruction/exercises. Neuromorpho.org is the first neuronal morphology database that provides qualitative and quantitative data from reconstructed cells analyzed in published scientific reports. The Neuromorpho.org database contains cross species and multiple neuronal phenotype datasets which allows for comparative examinations. The ABA provides modules that allow students to study the anatomy of the rodent brain, as well as observe the different cellular phenotypes that exist using histochemical labeling. Using these tools in conjunction, advanced students can ask questions about qualitative and quantitative neuronal morphology, then examine the distribution of the same cell types across the entire brain to gain a full appreciation of the magnitude of the brain's complexity.

  8. The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

    Science.gov (United States)

    Nowinski, Wieslaw L; Belov, Dmitry

    2003-09-01

    The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

  9. Stereoscopic Three-Dimensional Visualization Applied to Multimodal Brain Images: Clinical Applications and a Functional Connectivity Atlas.

    Directory of Open Access Journals (Sweden)

    Gonzalo M Rojas

    2014-11-01

    Full Text Available Effective visualization is central to the exploration and comprehension of brain imaging data. While MRI data are acquired in three-dimensional space, the methods for visualizing such data have rarely taken advantage of three-dimensional stereoscopic technologies. We present here results of stereoscopic visualization of clinical data, as well as an atlas of whole-brain functional connectivity. In comparison with traditional 3D rendering techniques, we demonstrate the utility of stereoscopic visualizations to provide an intuitive description of the exact location and the relative sizes of various brain landmarks, structures and lesions. In the case of resting state fMRI, stereoscopic 3D visualization facilitated comprehension of the anatomical position of complex large-scale functional connectivity patterns. Overall, stereoscopic visualization improves the intuitive visual comprehension of image contents, and brings increased dimensionality to visualization of traditional MRI data, as well as patterns of functional connectivity.

  10. 99mTc-HMPAO Brain SPECT in Seizure Disorder: Comparison Brain SPECT, MRI / CT and EEG

    International Nuclear Information System (INIS)

    Yang, Hyung In; Im, Ju Hyuk; Choi, Chang Woon; Lee, Dong Soo; Chung, June Key; No, Jae Kyu; Lee, Myung Chul; Koh, Chang Soon

    1994-01-01

    We studied 115 patients with seizure who had been performed brain SPECT brain MRI of CT and EEG. To evaluate the pattern of brain SPECT in seizure patients 28 of them had secondary epilepsies, 87 had primary epilepsies. In primary epilepsies, 42 were generalized seizure and 45 were partial seizure. The causes of secondary epilepsies were congenital malformation, cerebromalacia, cerebral infarction ultiple sclerosis, AV-malformation. granuloma and etc, in order. In 28 secondary epilepsies, 25 of them, brain SPECT lesions was concordant with MRI or CT lesions. 3 were disconcordant. The brain SPECT findings of generalized seizure were normal in 22 patients, diffuse irregular decreased perfusion in 8, decreased in frontal cortex in 4. temporal in 5 and frontotemporal in 3. In 45 partial seizure, 19 brain SPECT were concordant with EEG (42.4%).

  11. TECHNOLOGIES OF BRAIN IMAGES PROCESSING

    Directory of Open Access Journals (Sweden)

    O.M. Klyuchko

    2017-12-01

    Full Text Available The purpose of present research was to analyze modern methods of processing biological images implemented before storage in databases for biotechnological purposes. The databases further were incorporated into web-based digital systems. Examples of such information systems were described in the work for two levels of biological material organization; databases for storing data of histological analysis and of whole brain were described. Methods of neuroimaging processing for electronic brain atlas were considered. It was shown that certain pathological features can be revealed in histological image processing. Several medical diagnostic techniques (for certain brain pathologies, etc. as well as a few biotechnological methods are based on such effects. Algorithms of image processing were suggested. Electronic brain atlas was conveniently for professionals in different fields described in details. Approaches of brain atlas elaboration, “composite” scheme for large deformations as well as several methods of mathematic images processing were described as well.

  12. Generation of a 3D atlas of the nuclear division of the thalamus based on histological sections of primate: Intra- and intersubject atlas-to-MRI warping

    International Nuclear Information System (INIS)

    Dauguet, J.; Conde, F.; Hantraye, P.; Delzescaux, T.; Frouin, V.

    2009-01-01

    We describe a framework to generate a 3D digital atlas of the thalamus based on a series of stained histological sections of a primate. The contours of the thalamus were first drawn on the stained histological slices. The series of histological sections were then aligned and mapped onto the in vivo MRI of the same animal acquired prior to the sacrifice following a methodology described in Dauguet et al. (2007) using the block face photographs as an intermediary modality. By applying the series of transformations previously estimated for the histological volume, the contours of the digital atlas were mapped onto the MRI data. The protocol was tested on two baboon brains for which the full series of slices were available, and a macaque brain for which a subset only of the histological slices were available demonstrating the ability of building digital atlases in the MRI geometry without mounting and staining all the brain slices. We then studied the accuracy of mapping the digital atlas of one baboon onto the MRI of the other baboon by comparing the overlapping with its original digital atlas. We finally used the digital atlas of one of the baboons to study the individual kinetic of the main thalamus nuclei on Positron Emission Tomography (PET) images providing a novel and accurate way of measuring very fine and local functional differences. (authors)

  13. Unbiased group-wise image registration: applications in brain fiber tract atlas construction and functional connectivity analysis.

    Science.gov (United States)

    Geng, Xiujuan; Gu, Hong; Shin, Wanyong; Ross, Thomas J; Yang, Yihong

    2011-10-01

    We propose an unbiased implicit-reference group-wise (IRG) image registration method and demonstrate its applications in the construction of a brain white matter fiber tract atlas and the analysis of resting-state functional MRI (fMRI) connectivity. Most image registration techniques pair-wise align images to a selected reference image and group analyses are performed in the reference space, which may produce bias. The proposed method jointly estimates transformations, with an elastic deformation model, registering all images to an implicit reference corresponding to the group average. The unbiased registration is applied to build a fiber tract atlas by registering a group of diffusion tensor images. Compared to reference-based registration, the IRG registration improves the fiber track overlap within the group. After applying the method in the fMRI connectivity analysis, results suggest a general improvement in functional connectivity maps at a group level in terms of larger cluster size and higher average t-scores.

  14. Spatially adapted augmentation of age-specific atlas-based segmentation using patch-based priors

    Science.gov (United States)

    Liu, Mengyuan; Seshamani, Sharmishtaa; Harrylock, Lisa; Kitsch, Averi; Miller, Steven; Chau, Van; Poskitt, Kenneth; Rousseau, Francois; Studholme, Colin

    2014-03-01

    One of the most common approaches to MRI brain tissue segmentation is to employ an atlas prior to initialize an Expectation- Maximization (EM) image labeling scheme using a statistical model of MRI intensities. This prior is commonly derived from a set of manually segmented training data from the population of interest. However, in cases where subject anatomy varies significantly from the prior anatomical average model (for example in the case where extreme developmental abnormalities or brain injuries occur), the prior tissue map does not provide adequate information about the observed MRI intensities to ensure the EM algorithm converges to an anatomically accurate labeling of the MRI. In this paper, we present a novel approach for automatic segmentation of such cases. This approach augments the atlas-based EM segmentation by exploring methods to build a hybrid tissue segmentation scheme that seeks to learn where an atlas prior fails (due to inadequate representation of anatomical variation in the statistical atlas) and utilize an alternative prior derived from a patch driven search of the atlas data. We describe a framework for incorporating this patch-based augmentation of EM (PBAEM) into a 4D age-specific atlas-based segmentation of developing brain anatomy. The proposed approach was evaluated on a set of MRI brain scans of premature neonates with ages ranging from 27.29 to 46.43 gestational weeks (GWs). Results indicated superior performance compared to the conventional atlas-based segmentation method, providing improved segmentation accuracy for gray matter, white matter, ventricles and sulcal CSF regions.

  15. {sup 99m}Tc-HMPAO Brain SPECT in Seizure Disorder: Comparison Brain SPECT, MRI / CT and EEG

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hyung In [Kyunghee University Hospital, Seoul (Korea, Republic of); Im, Ju Hyuk; Choi, Chang Woon; Lee, Dong Soo; Chung, June Key; No, Jae Kyu; Lee, Myung Chul; Koh, Chang Soon [Seoul National University Hospital, Seoul (Korea, Republic of)

    1994-03-15

    We studied 115 patients with seizure who had been performed brain SPECT brain MRI of CT and EEG. To evaluate the pattern of brain SPECT in seizure patients 28 of them had secondary epilepsies, 87 had primary epilepsies. In primary epilepsies, 42 were generalized seizure and 45 were partial seizure. The causes of secondary epilepsies were congenital malformation, cerebromalacia, cerebral infarction ultiple sclerosis, AV-malformation. granuloma and etc, in order. In 28 secondary epilepsies, 25 of them, brain SPECT lesions was concordant with MRI or CT lesions. 3 were disconcordant. The brain SPECT findings of generalized seizure were normal in 22 patients, diffuse irregular decreased perfusion in 8, decreased in frontal cortex in 4. temporal in 5 and frontotemporal in 3. In 45 partial seizure, 19 brain SPECT were concordant with EEG (42.4%).

  16. Atlas warping for brain morphometry

    Science.gov (United States)

    Machado, Alexei M. C.; Gee, James C.

    1998-06-01

    In this work, we describe an automated approach to morphometry based on spatial normalizations of the data, and demonstrate its application to the analysis of gender differences in the human corpus callosum. The purpose is to describe a population by a reduced and representative set of variables, from which a prior model can be constructed. Our approach is rooted in the assumption that individual anatomies can be considered as quantitative variations on a common underlying qualitative plane. We can therefore imagine that a given individual's anatomy is a warped version of some referential anatomy, also known as an atlas. The spatial warps which transform a labeled atlas into anatomic alignment with a population yield immediate knowledge about organ size and shape in the group. Furthermore, variation within the set of spatial warps is directly related to the anatomic variation among the subjects. Specifically, the shape statistics--mean and variance of the mappings--for the population can be calculated in a special basis, and an eigendecomposition of the variance performed to identify the most significant modes of shape variation. The results obtained with the corpus callosum study confirm the existence of substantial anatomical differences between males and females, as reported in previous experimental work.

  17. The Hatfield SCT lunar atlas photographic atlas for Meade, Celestron, and other SCT telescopes

    CERN Document Server

    2014-01-01

    In a major publishing event for lunar observers, the justly famous Hatfield atlas is updated in even more usable form. This version of Hatfield’s classic atlas solves the problem of mirror images, making identification of left-right reversed imaged lunar features both quick and easy. SCT and Maksutov telescopes – which of course include the best-selling models from Meade and Celestron – reverse the visual image left to right. Thus it is extremely difficult to identify lunar features at the eyepiece of one of the instruments using a conventional Moon atlas, as the human brain does not cope well when trying to compare the real thing with a map that is a mirror image of it. Now this issue has at last been solved.   In this atlas the Moon’s surface is shown at various sun angles, and inset keys show the effects of optical librations. Smaller non-mirrored reference images are also included to make it simple to compare the mirrored SCT plates and maps with those that appear in other atlases. This edition s...

  18. A novel approach of fMRI-guided tractography analysis within a group: construction of an fMRI-guided tractographic atlas.

    Science.gov (United States)

    Preti, Maria Giulia; Makris, Nikos; Laganà, Maria Marcella; Papadimitriou, George; Baglio, Francesca; Griffanti, Ludovica; Nemni, Raffaello; Cecconi, Pietro; Westin, Carl-Fredrik; Baselli, Giuseppe

    2012-01-01

    Diffusion Tensor Imaging (DTI) tractography and functional Magnetic Resonance Imaging (fMRI) investigate two complementary aspects of brain networks: white matter (WM) anatomical connectivity and gray matter (GM) function. However, integration standards have yet to be defined; namely, individual fMRI-driven tractography is usually applied and only few studies address group analysis. This work proposes an efficient method of fMRI-driven tractography at group level through the creation of a tractographic atlas starting from the GM areas activated by a verbal fluency task in 11 healthy subjects. The individual tracts were registered to the MNI space. Selection ROIs derived by GM masking and dilation of group activated areas were applied to obtain the fMRI-driven subsets within tracts. An atlas of the tracts recruited among the population was obtained by selecting for each subject the fMRI-guided tracts passing through the high probability voxels (the voxels recruited by the 90% of the subjects) and merging them together. The reliability of this approach was assessed by comparing it with the probabilistic atlas previously introduced in literature. The introduced method allowed to successfully reconstruct activated tracts, which comprehended corpus callosum, left cingulum and arcuate, a small portion of the right arcuate, both cortico-spinal tracts and inferior fronto-occipital fasciculi. Moreover, it proved to give results concordant with the previously introduced probabilistic approach, allowing in addition to reconstruct 3D trajectories of the activated fibers, which appear particularly helpful in the detection of WM connections.

  19. Repeatability of Brain Volume Measurements Made with the Atlas-based Method from T1-weighted Images Acquired Using a 0.4 Tesla Low Field MR Scanner.

    Science.gov (United States)

    Goto, Masami; Suzuki, Makoto; Mizukami, Shinya; Abe, Osamu; Aoki, Shigeki; Miyati, Tosiaki; Fukuda, Michinari; Gomi, Tsutomu; Takeda, Tohoru

    2016-10-11

    An understanding of the repeatability of measured results is important for both the atlas-based and voxel-based morphometry (VBM) methods of magnetic resonance (MR) brain volumetry. However, many recent studies that have investigated the repeatability of brain volume measurements have been performed using static magnetic fields of 1-4 tesla, and no study has used a low-strength static magnetic field. The aim of this study was to investigate the repeatability of measured volumes using the atlas-based method and a low-strength static magnetic field (0.4 tesla). Ten healthy volunteers participated in this study. Using a 0.4 tesla magnetic resonance imaging (MRI) scanner and a quadrature head coil, three-dimensional T 1 -weighted images (3D-T 1 WIs) were obtained from each subject, twice on the same day. VBM8 software was used to construct segmented normalized images [gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) images]. The regions-of-interest (ROIs) of GM, WM, CSF, hippocampus (HC), orbital gyrus (OG), and cerebellum posterior lobe (CPL) were generated using WFU PickAtlas. The percentage change was defined as[100 × (measured volume with first segmented image - mean volume in each subject)/(mean volume in each subject)]The average percentage change was calculated as the percentage change in the 6 ROIs of the 10 subjects. The mean of the average percentage changes for each ROI was as follows: GM, 0.556%; WM, 0.324%; CSF, 0.573%; HC, 0.645%; OG, 1.74%; and CPL, 0.471%. The average percentage change was higher for the orbital gyrus than for the other ROIs. We consider that repeatability of the atlas-based method is similar between 0.4 and 1.5 tesla MR scanners. To our knowledge, this is the first report to show that the level of repeatability with a 0.4 tesla MR scanner is adequate for the estimation of brain volume change by the atlas-based method.

  20. In vivo quantitative whole-brain diffusion tensor imaging analysis of APP/PS1 transgenic mice using voxel-based and atlas-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Yuan-Yuan [Huazhong University of Science and Technology, Department of Radiology, Tongji Hospital, Tongji Medical College, Wuhan (China); The Johns Hopkins University School of Medicine, The Russell H. Morgan Department of Radiology and Radiological Science, Baltimore, MD (United States); Li, Mu-Wei; Oishi, Kenichi [The Johns Hopkins University School of Medicine, The Russell H. Morgan Department of Radiology and Radiological Science, Baltimore, MD (United States); Zhang, Shun; Zhang, Yan; Zhao, Ling-Yun; Zhu, Wen-Zhen [Huazhong University of Science and Technology, Department of Radiology, Tongji Hospital, Tongji Medical College, Wuhan (China); Lei, Hao [Chinese Academy of Sciences, Wuhan Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Wuhan (China)

    2013-08-15

    Diffusion tensor imaging (DTI) has been applied to characterize the pathological features of Alzheimer's disease (AD) in a mouse model, although little is known about whether these features are structure specific. Voxel-based analysis (VBA) and atlas-based analysis (ABA) are good complementary tools for whole-brain DTI analysis. The purpose of this study was to identify the spatial localization of disease-related pathology in an AD mouse model. VBA and ABA quantification were used for the whole-brain DTI analysis of nine APP/PS1 mice and wild-type (WT) controls. Multiple scalar measurements, including fractional anisotropy (FA), trace, axial diffusivity (DA), and radial diffusivity (DR), were investigated to capture the various types of pathology. The accuracy of the image transformation applied for VBA and ABA was evaluated by comparing manual and atlas-based structure delineation using kappa statistics. Following the MR examination, the brains of the animals were analyzed for microscopy. Extensive anatomical alterations were identified in APP/PS1 mice, in both the gray matter areas (neocortex, hippocampus, caudate putamen, thalamus, hypothalamus, claustrum, amygdala, and piriform cortex) and the white matter areas (corpus callosum/external capsule, cingulum, septum, internal capsule, fimbria, and optic tract), evidenced by an increase in FA or DA, or both, compared to WT mice (p < 0.05, corrected). The average kappa value between manual and atlas-based structure delineation was approximately 0.8, and there was no significant difference between APP/PS1 and WT mice (p > 0.05). The histopathological changes in the gray matter areas were confirmed by microscopy studies. DTI did, however, demonstrate significant changes in white matter areas, where the difference was not apparent by qualitative observation of a single-slice histological specimen. This study demonstrated the structure-specific nature of pathological changes in APP/PS1 mouse, and also showed the

  1. Two-stage atlas subset selection in multi-atlas based image segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Tingting, E-mail: tingtingzhao@mednet.ucla.edu; Ruan, Dan, E-mail: druan@mednet.ucla.edu [The Department of Radiation Oncology, University of California, Los Angeles, California 90095 (United States)

    2015-06-15

    Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

  2. Two-stage atlas subset selection in multi-atlas based image segmentation.

    Science.gov (United States)

    Zhao, Tingting; Ruan, Dan

    2015-06-01

    Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. The authors have developed a novel two-stage atlas

  3. Two-stage atlas subset selection in multi-atlas based image segmentation

    International Nuclear Information System (INIS)

    Zhao, Tingting; Ruan, Dan

    2015-01-01

    Purpose: Fast growing access to large databases and cloud stored data presents a unique opportunity for multi-atlas based image segmentation and also presents challenges in heterogeneous atlas quality and computation burden. This work aims to develop a novel two-stage method tailored to the special needs in the face of large atlas collection with varied quality, so that high-accuracy segmentation can be achieved with low computational cost. Methods: An atlas subset selection scheme is proposed to substitute a significant portion of the computationally expensive full-fledged registration in the conventional scheme with a low-cost alternative. More specifically, the authors introduce a two-stage atlas subset selection method. In the first stage, an augmented subset is obtained based on a low-cost registration configuration and a preliminary relevance metric; in the second stage, the subset is further narrowed down to a fusion set of desired size, based on full-fledged registration and a refined relevance metric. An inference model is developed to characterize the relationship between the preliminary and refined relevance metrics, and a proper augmented subset size is derived to ensure that the desired atlases survive the preliminary selection with high probability. Results: The performance of the proposed scheme has been assessed with cross validation based on two clinical datasets consisting of manually segmented prostate and brain magnetic resonance images, respectively. The proposed scheme demonstrates comparable end-to-end segmentation performance as the conventional single-stage selection method, but with significant computation reduction. Compared with the alternative computation reduction method, their scheme improves the mean and medium Dice similarity coefficient value from (0.74, 0.78) to (0.83, 0.85) and from (0.82, 0.84) to (0.95, 0.95) for prostate and corpus callosum segmentation, respectively, with statistical significance. Conclusions: The authors

  4. Connecting imaging mass spectrometry and magnetic resonance imaging-based anatomical atlases for automated anatomical interpretation and differential analysis.

    Science.gov (United States)

    Verbeeck, Nico; Spraggins, Jeffrey M; Murphy, Monika J M; Wang, Hui-Dong; Deutch, Ariel Y; Caprioli, Richard M; Van de Plas, Raf

    2017-07-01

    Imaging mass spectrometry (IMS) is a molecular imaging technology that can measure thousands of biomolecules concurrently without prior tagging, making it particularly suitable for exploratory research. However, the data size and dimensionality often makes thorough extraction of relevant information impractical. To help guide and accelerate IMS data analysis, we recently developed a framework that integrates IMS measurements with anatomical atlases, opening up opportunities for anatomy-driven exploration of IMS data. One example is the automated anatomical interpretation of ion images, where empirically measured ion distributions are automatically decomposed into their underlying anatomical structures. While offering significant potential, IMS-atlas integration has thus far been restricted to the Allen Mouse Brain Atlas (AMBA) and mouse brain samples. Here, we expand the applicability of this framework by extending towards new animal species and a new set of anatomical atlases retrieved from the Scalable Brain Atlas (SBA). Furthermore, as many SBA atlases are based on magnetic resonance imaging (MRI) data, a new registration pipeline was developed that enables direct non-rigid IMS-to-MRI registration. These developments are demonstrated on protein-focused FTICR IMS measurements from coronal brain sections of a Parkinson's disease (PD) rat model. The measurements are integrated with an MRI-based rat brain atlas from the SBA. The new rat-focused IMS-atlas integration is used to perform automated anatomical interpretation and to find differential ions between healthy and diseased tissue. IMS-atlas integration can serve as an important accelerator in IMS data exploration, and with these new developments it can now be applied to a wider variety of animal species and modalities. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann. Copyright © 2017. Published by Elsevier B.V.

  5. Brain areas associated with numbers and calculations in children: Meta-analyses of fMRI studies

    Directory of Open Access Journals (Sweden)

    Marie Arsalidou

    2018-04-01

    Full Text Available Children use numbers every day and typically receive formal mathematical training from an early age, as it is a main subject in school curricula. Despite an increase in children neuroimaging studies, a comprehensive neuropsychological model of mathematical functions in children is lacking. Using quantitative meta-analyses of functional magnetic resonance imaging (fMRI studies, we identify concordant brain areas across articles that adhere to a set of selection criteria (e.g., whole-brain analysis, coordinate reports and report brain activity to tasks that involve processing symbolic and non-symbolic numbers with and without formal mathematical operations, which we called respectively number tasks and calculation tasks. We present data on children 14 years and younger, who solved these tasks. Results show activity in parietal (e.g., inferior parietal lobule and precuneus and frontal (e.g., superior and medial frontal gyri cortices, core areas related to mental-arithmetic, as well as brain regions such as the insula and claustrum, which are not typically discussed as part of mathematical problem solving models. We propose a topographical atlas of mathematical processes in children, discuss findings within a developmental constructivist theoretical model, and suggest practical methodological considerations for future studies. Keywords: Mathematical cognition, Meta-analyses, fMRI, Children, Development, Insula

  6. MRI-based treatment planning with pseudo CT generated through atlas registration.

    Science.gov (United States)

    Uh, Jinsoo; Merchant, Thomas E; Li, Yimei; Li, Xingyu; Hua, Chiaho

    2014-05-01

    To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787-0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%-98.7%) satisfied the criteria of chi-evaluation (pediatric brain tumor patients. The doses calculated from pseudo CTs agreed well with those from real CTs

  7. Quantification of 18F-FDG PET images using probabilistic brain atlas: clinical application in temporal lobe epilepsy patients

    International Nuclear Information System (INIS)

    Kang, Keon Wook; Lee, Dong Soo; Cho, Jae Hoon; Lee, Jae Sung; Yeo, Jeong Seok; Lee, Sang Gun; Chung, June Key; Lee, Myung Chul

    2000-01-01

    A probabilistic atlas of the human brain (Statistical Probability Anatomical Maps: SPAM) was developed by the international consortium for brain mapping (ICBM). After calculating the counts in volume of interest (VOI) using the product of probability of SPAM images and counts in FDG images, asymmetric indexes(AI) were calculated and used for finding epileptogenic zones in temporal lobe epilepsy (TLE). FDG PET images from 28 surgically confirmed TLE patients and 12 age-matched controls were spatially normalized to the averaged brain MRI atlas of ICBM. The counts from normalized PET images were multiplied with the probability of 12 VOIs (superior temporal gyrus, middle temporal gyrus, inferior temporal gyrus, hippocampus, parahippocampal gyrus, and amygdala in each hemisphere) of SPAM images of Montreal Neurological Institute. Finally AI was calculated on each pair of VOI, and compared with visual assessment. If AI was deviated more than 2 standard deviation of normal controls, we considered epileptogenic zones were found successfully. The counts of VOIs in normal controls were symmetric (AI 0.05) except those of inferior temporal gyrus (p<0.01). AIs in 5 pairs of VOI excluding inferior temporal gyrus were deviated to one side in TLE (p<0.05). Lateralization was correct in 23/28 of patients by AI, but all of 28 were consistent with visual inspection. In 3 patients with normal AI was symmetric on visual inspection. In 2 patients falsely lateralized using AI, metabolism was also decreased visually on contra-lateral side. Asymmetric index obtained by the product of statistical probability anatomical map and FDG PET correlated well with visual assessment in TLE patients. SPAM is useful for quantification of VOIs in functional images

  8. Anatomical guidance for functional near-infrared spectroscopy: AtlasViewer tutorial.

    Science.gov (United States)

    Aasted, Christopher M; Yücel, Meryem A; Cooper, Robert J; Dubb, Jay; Tsuzuki, Daisuke; Becerra, Lino; Petkov, Mike P; Borsook, David; Dan, Ippeita; Boas, David A

    2015-04-01

    Functional near-infrared spectroscopy (fNIRS) is an optical imaging method that is used to noninvasively measure cerebral hemoglobin concentration changes induced by brain activation. Using structural guidance in fNIRS research enhances interpretation of results and facilitates making comparisons between studies. AtlasViewer is an open-source software package we have developed that incorporates multiple spatial registration tools to enable structural guidance in the interpretation of fNIRS studies. We introduce the reader to the layout of the AtlasViewer graphical user interface, the folder structure, and user files required in the creation of fNIRS probes containing sources and detectors registered to desired locations on the head, evaluating probe fabrication error and intersubject probe placement variability, and different procedures for estimating measurement sensitivity to different brain regions as well as image reconstruction performance. Further, we detail how AtlasViewer provides a generic head atlas for guiding interpretation of fNIRS results, but also permits users to provide subject-specific head anatomies to interpret their results. We anticipate that AtlasViewer will be a valuable tool in improving the anatomical interpretation of fNIRS studies.

  9. Fast and robust multi-atlas segmentation of brain magnetic resonance images

    DEFF Research Database (Denmark)

    Lötjönen, Jyrki Mp; Wolz, Robin; Koikkalainen, Juha R

    2010-01-01

    of standard normalised mutual information in registration without compromising the accuracy but leading to threefold decrease in the computation time. We study and validate also different methods for atlas selection. Finally, we propose two new approaches for combining multi-atlas segmentation and intensity...

  10. On the concordance genus of topologically slice knots

    OpenAIRE

    Hom, Jennifer

    2012-01-01

    The concordance genus of a knot K is the minimum Seifert genus of all knots smoothly concordant to K. Concordance genus is bounded below by the 4-ball genus and above by the Seifert genus. We give a lower bound for the concordance genus of K coming from the knot Floer complex of K. As an application, we prove that there are topologically slice knots with 4-ball genus equal to one and arbitrarily large concordance genus.

  11. Atlas based brain volumetry: How to distinguish regional volume changes due to biological or physiological effects from inherent noise of the methodology.

    Science.gov (United States)

    Opfer, Roland; Suppa, Per; Kepp, Timo; Spies, Lothar; Schippling, Sven; Huppertz, Hans-Jürgen

    2016-05-01

    Fully-automated regional brain volumetry based on structural magnetic resonance imaging (MRI) plays an important role in quantitative neuroimaging. In clinical trials as well as in clinical routine multiple MRIs of individual patients at different time points need to be assessed longitudinally. Measures of inter- and intrascanner variability are crucial to understand the intrinsic variability of the method and to distinguish volume changes due to biological or physiological effects from inherent noise of the methodology. To measure regional brain volumes an atlas based volumetry (ABV) approach was deployed using a highly elastic registration framework and an anatomical atlas in a well-defined template space. We assessed inter- and intrascanner variability of the method in 51 cognitively normal subjects and 27 Alzheimer dementia (AD) patients from the Alzheimer's Disease Neuroimaging Initiative by studying volumetric results of repeated scans for 17 compartments and brain regions. Median percentage volume differences of scan-rescans from the same scanner ranged from 0.24% (whole brain parenchyma in healthy subjects) to 1.73% (occipital lobe white matter in AD), with generally higher differences in AD patients as compared to normal subjects (e.g., 1.01% vs. 0.78% for the hippocampus). Minimum percentage volume differences detectable with an error probability of 5% were in the one-digit percentage range for almost all structures investigated, with most of them being below 5%. Intrascanner variability was independent of magnetic field strength. The median interscanner variability was up to ten times higher than the intrascanner variability. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. New experimental results in atlas-based brain morphometry

    Science.gov (United States)

    Gee, James C.; Fabella, Brian A.; Fernandes, Siddharth E.; Turetsky, Bruce I.; Gur, Ruben C.; Gur, Raquel E.

    1999-05-01

    In a previous meeting, we described a computational approach to MRI morphometry, in which a spatial warp mapping a reference or atlas image into anatomic alignment with the subject is first inferred. Shape differences with respect to the atlas are then studied by calculating the pointwise Jacobian determinant for the warp, which provides a measure of the change in differential volume about a point in the reference as it transforms to its corresponding position in the subject. In this paper, the method is used to analyze sex differences in the shape and size of the corpus callosum in an ongoing study of a large population of normal controls. The preliminary results of the current analysis support findings in the literature that have observed the splenium to be larger in females than in males.

  13. Bridging neuroanatomy, neuroradiology and neurology: three-dimensional interactive atlas of neurological disorders.

    Science.gov (United States)

    Nowinski, W L; Chua, B C

    2013-06-01

    Understanding brain pathology along with the underlying neuroanatomy and the resulting neurological deficits is of vital importance in medical education and clinical practice. To facilitate and expedite this understanding, we created a three-dimensional (3D) interactive atlas of neurological disorders providing the correspondence between a brain lesion and the resulting disorder(s). The atlas contains a 3D highly parcellated atlas of normal neuroanatomy along with a brain pathology database. Normal neuroanatomy is divided into about 2,300 components, including the cerebrum, cerebellum, brainstem, spinal cord, arteries, veins, dural sinuses, tracts, cranial nerves (CN), white matter, deep gray nuclei, ventricles, visual system, muscles, glands and cervical vertebrae (C1-C5). The brain pathology database contains 144 focal and distributed synthesized lesions (70 vascular, 36 CN-related, and 38 regional anatomy-related), each lesion labeled with the resulting disorder and associated signs, symptoms, and/or syndromes compiled from materials reported in the literature. The initial view of each lesion was preset in terms of its location and size, surrounding surface and sectional (magnetic resonance) neuroanatomy, and labeling of lesion and neuroanatomy. In addition, a glossary of neurological disorders was compiled and for each disorder materials from textbooks were included to provide neurological description. This atlas of neurological disorders is potentially useful to a wide variety of users ranging from medical students, residents and nurses to general practitioners, neuroanatomists, neuroradiologists and neurologists, as it contains both normal (surface and sectional) brain anatomy and pathology correlated with neurological disorders presented in a visual and interactive way.

  14. Atlas selection for hippocampus segmentation: Relevance evaluation of three meta-information parameters.

    Science.gov (United States)

    Dill, Vanderson; Klein, Pedro Costa; Franco, Alexandre Rosa; Pinho, Márcio Sarroglia

    2018-04-01

    Current state-of-the-art methods for whole and subfield hippocampus segmentation use pre-segmented templates, also known as atlases, in the pre-processing stages. Typically, the input image is registered to the template, which provides prior information for the segmentation process. Using a single standard atlas increases the difficulty in dealing with individuals who have a brain anatomy that is morphologically different from the atlas, especially in older brains. To increase the segmentation precision in these cases, without any manual intervention, multiple atlases can be used. However, registration to many templates leads to a high computational cost. Researchers have proposed to use an atlas pre-selection technique based on meta-information followed by the selection of an atlas based on image similarity. Unfortunately, this method also presents a high computational cost due to the image-similarity process. Thus, it is desirable to pre-select a smaller number of atlases as long as this does not impact on the segmentation quality. To pick out an atlas that provides the best registration, we evaluate the use of three meta-information parameters (medical condition, age range, and gender) to choose the atlas. In this work, 24 atlases were defined and each is based on the combination of the three meta-information parameters. These atlases were used to segment 352 vol from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Hippocampus segmentation with each of these atlases was evaluated and compared to reference segmentations of the hippocampus, which are available from ADNI. The use of atlas selection by meta-information led to a significant gain in the Dice similarity coefficient, which reached 0.68 ± 0.11, compared to 0.62 ± 0.12 when using only the standard MNI152 atlas. Statistical analysis showed that the three meta-information parameters provided a significant improvement in the segmentation accuracy. Copyright © 2018 Elsevier Ltd

  15. Evaluation of atlas-based auto-segmentation software in prostate cancer patients

    International Nuclear Information System (INIS)

    Greenham, Stuart; Dean, Jenna; Fu, Cheuk Kuen Kenneth; Goman, Joanne; Mulligan, Jeremy; Tune, Deanna; Sampson, David; Westhuyzen, Justin; McKay, Michael

    2014-01-01

    The performance and limitations of an atlas-based auto-segmentation software package (ABAS; Elekta Inc.) was evaluated using male pelvic anatomy as the area of interest. Contours from 10 prostate patients were selected to create atlases in ABAS. The contoured regions of interest were created manually to align with published guidelines and included the prostate, bladder, rectum, femoral heads and external patient contour. Twenty-four clinically treated prostate patients were auto-contoured using a randomised selection of two, four, six, eight or ten atlases. The concordance between the manually drawn and computer-generated contours were evaluated statistically using Pearson's product–moment correlation coefficient (r) and clinically in a validated qualitative evaluation. In the latter evaluation, six radiation therapists classified the degree of agreement for each structure using seven clinically appropriate categories. The ABAS software generated clinically acceptable contours for the bladder, rectum, femoral heads and external patient contour. For these structures, ABAS-generated volumes were highly correlated with ‘as treated’ volumes, manually drawn; for four atlases, for example, bladder r = 0.988 (P < 0.001), rectum r = 0.739 (P < 0.001) and left femoral head r = 0.560 (P < 0.001). Poorest results were seen for the prostate (r = 0.401, P < 0.05) (four atlases); however this was attributed to the comparison prostate volume being contoured on magnetic resonance imaging (MRI) rather than computed tomography (CT) data. For all structures, increasing the number of atlases did not consistently improve accuracy. ABAS-generated contours are clinically useful for a range of structures in the male pelvis. Clinically appropriate volumes were created, but editing of some contours was inevitably required. The ideal number of atlases to improve generated automatic contours is yet to be determined

  16. The hatfield SCT lunar atlas photographic atlas for Meade, Celestron and other SCT telescopes

    CERN Document Server

    Cook, Jeremy

    2005-01-01

    Schmitt-Cassegrain Telescopes (SCT) and Schmitt-Maksutov telescopes - which include the best-selling models from Meade, Celestron, and other important manufacturers - reverse the visual image left for right, giving a "mirror image". This makes it extremely difficult for observers to identify lunar features at the eyepiece of one of these instruments, using conventional atlases which show the Moon "upside-down" with south at the top. The human brain just doesn't cope well with trying to compare the real thing with a map that is a mirror-image of it!The Hatfield SCT Lunar Atlas solves the problem. Photographs and the detailed key maps are exactly as the Moon appears through the eyepiece of an SCT or Maksutov telescope. Smaller IAU-standard reference photographs are included on each page, to make it simple to compare the mirrored SCT photographs and maps with those that appear in other conventional atlases.Every owner of an SCT - and that's most amateur astronomers - will want this!.

  17. An anatomic transcriptional atlas of human glioblastoma.

    Science.gov (United States)

    Puchalski, Ralph B; Shah, Nameeta; Miller, Jeremy; Dalley, Rachel; Nomura, Steve R; Yoon, Jae-Guen; Smith, Kimberly A; Lankerovich, Michael; Bertagnolli, Darren; Bickley, Kris; Boe, Andrew F; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Chapin, Mike; Datta, Suvro; Dee, Nick; Desta, Tsega; Dolbeare, Tim; Dotson, Nadezhda; Ebbert, Amanda; Feng, David; Feng, Xu; Fisher, Michael; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W; Gu, Guangyu; Hejazinia, Nika; Hohmann, John; Hothi, Parvinder; Howard, Robert; Joines, Kevin; Kriedberg, Ali; Kuan, Leonard; Lau, Chris; Lee, Felix; Lee, Hwahyung; Lemon, Tracy; Long, Fuhui; Mastan, Naveed; Mott, Erika; Murthy, Chantal; Ngo, Kiet; Olson, Eric; Reding, Melissa; Riley, Zack; Rosen, David; Sandman, David; Shapovalova, Nadiya; Slaughterbeck, Clifford R; Sodt, Andrew; Stockdale, Graham; Szafer, Aaron; Wakeman, Wayne; Wohnoutka, Paul E; White, Steven J; Marsh, Don; Rostomily, Robert C; Ng, Lydia; Dang, Chinh; Jones, Allan; Keogh, Bart; Gittleman, Haley R; Barnholtz-Sloan, Jill S; Cimino, Patrick J; Uppin, Megha S; Keene, C Dirk; Farrokhi, Farrokh R; Lathia, Justin D; Berens, Michael E; Iavarone, Antonio; Bernard, Amy; Lein, Ed; Phillips, John W; Rostad, Steven W; Cobbs, Charles; Hawrylycz, Michael J; Foltz, Greg D

    2018-05-11

    Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  18. PREDICTING APHASIA TYPE FROM BRAIN DAMAGE MEASURED WITH STRUCTURAL MRI

    Science.gov (United States)

    Yourganov, Grigori; Smith, Kimberly G.; Fridriksson, Julius; Rorden, Chris

    2015-01-01

    Chronic aphasia is a common consequence of a left-hemisphere stroke. Since the early insights by Broca and Wernicke, studying the relationship between the loci of cortical damage and patterns of language impairment has been one of the concerns of aphasiology. We utilized multivariate classification in a cross-validation framework to predict the type of chronic aphasia from the spatial pattern of brain damage. Our sample consisted of 98 patients with five types of aphasia (Broca’s, Wernicke’s, global, conduction, and anomic), classified based on scores on the Western Aphasia Battery. Binary lesion maps were obtained from structural MRI scans (obtained at least 6 months poststroke, and within 2 days of behavioural assessment); after spatial normalization, the lesions were parcellated into a disjoint set of brain areas. The proportion of damage to the brain areas was used to classify patients’ aphasia type. To create this parcellation, we relied on five brain atlases; our classifier (support vector machine) could differentiate between different kinds of aphasia using any of the five parcellations. In our sample, the best classification accuracy was obtained when using a novel parcellation that combined two previously published brain atlases, with the first atlas providing the segmentation of grey matter, and the second atlas used to segment the white matter. For each aphasia type, we computed the relative importance of different brain areas for distinguishing it from other aphasia types; our findings were consistent with previously published reports of lesion locations implicated in different types of aphasia. Overall, our results revealed that automated multivariate classification could distinguish between aphasia types based on damage to atlas-defined brain areas. PMID:26465238

  19. Predicting aphasia type from brain damage measured with structural MRI.

    Science.gov (United States)

    Yourganov, Grigori; Smith, Kimberly G; Fridriksson, Julius; Rorden, Chris

    2015-12-01

    Chronic aphasia is a common consequence of a left-hemisphere stroke. Since the early insights by Broca and Wernicke, studying the relationship between the loci of cortical damage and patterns of language impairment has been one of the concerns of aphasiology. We utilized multivariate classification in a cross-validation framework to predict the type of chronic aphasia from the spatial pattern of brain damage. Our sample consisted of 98 patients with five types of aphasia (Broca's, Wernicke's, global, conduction, and anomic), classified based on scores on the Western Aphasia Battery (WAB). Binary lesion maps were obtained from structural MRI scans (obtained at least 6 months poststroke, and within 2 days of behavioural assessment); after spatial normalization, the lesions were parcellated into a disjoint set of brain areas. The proportion of damage to the brain areas was used to classify patients' aphasia type. To create this parcellation, we relied on five brain atlases; our classifier (support vector machine - SVM) could differentiate between different kinds of aphasia using any of the five parcellations. In our sample, the best classification accuracy was obtained when using a novel parcellation that combined two previously published brain atlases, with the first atlas providing the segmentation of grey matter, and the second atlas used to segment the white matter. For each aphasia type, we computed the relative importance of different brain areas for distinguishing it from other aphasia types; our findings were consistent with previously published reports of lesion locations implicated in different types of aphasia. Overall, our results revealed that automated multivariate classification could distinguish between aphasia types based on damage to atlas-defined brain areas. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Quantification of {sup 18}F-FDG PET images using probabilistic brain atlas: clinical application in temporal lobe epilepsy patients

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Keon Wook; Lee, Dong Soo; Cho, Jae Hoon; Lee, Jae Sung; Yeo, Jeong Seok; Lee, Sang Gun; Chung, June Key; Lee, Myung Chul [Seoul National Univ., Seoul (Korea, Republic of)

    2000-07-01

    A probabilistic atlas of the human brain (Statistical Probability Anatomical Maps: SPAM) was developed by the international consortium for brain mapping (ICBM). After calculating the counts in volume of interest (VOI) using the product of probability of SPAM images and counts in FDG images, asymmetric indexes(AI) were calculated and used for finding epileptogenic zones in temporal lobe epilepsy (TLE). FDG PET images from 28 surgically confirmed TLE patients and 12 age-matched controls were spatially normalized to the averaged brain MRI atlas of ICBM. The counts from normalized PET images were multiplied with the probability of 12 VOIs (superior temporal gyrus, middle temporal gyrus, inferior temporal gyrus, hippocampus, parahippocampal gyrus, and amygdala in each hemisphere) of SPAM images of Montreal Neurological Institute. Finally AI was calculated on each pair of VOI, and compared with visual assessment. If AI was deviated more than 2 standard deviation of normal controls, we considered epileptogenic zones were found successfully. The counts of VOIs in normal controls were symmetric (AI <6%, paired t-test p>0.05) except those of inferior temporal gyrus (p<0.01). AIs in 5 pairs of VOI excluding inferior temporal gyrus were deviated to one side in TLE (p<0.05). Lateralization was correct in 23/28 of patients by AI, but all of 28 were consistent with visual inspection. In 3 patients with normal AI was symmetric on visual inspection. In 2 patients falsely lateralized using AI, metabolism was also decreased visually on contra-lateral side. Asymmetric index obtained by the product of statistical probability anatomical map and FDG PET correlated well with visual assessment in TLE patients. SPAM is useful for quantification of VOIs in functional images.

  1. Negative ... concord?

    NARCIS (Netherlands)

    Giannakidou, A

    The main claim of this paper is that a general theory of negative concord (NC) should allow for the possibility of NC involving scoping of a universal quantifier above negation. I propose that Greek NC instantiates this option. Greek n-words will be analyzed as polarity sensitive universal

  2. Multi-scale hippocampal parcellation improves atlas-based segmentation accuracy

    Science.gov (United States)

    Plassard, Andrew J.; McHugo, Maureen; Heckers, Stephan; Landman, Bennett A.

    2017-02-01

    Known for its distinct role in memory, the hippocampus is one of the most studied regions of the brain. Recent advances in magnetic resonance imaging have allowed for high-contrast, reproducible imaging of the hippocampus. Typically, a trained rater takes 45 minutes to manually trace the hippocampus and delineate the anterior from the posterior segment at millimeter resolution. As a result, there has been a significant desire for automated and robust segmentation of the hippocampus. In this work we use a population of 195 atlases based on T1-weighted MR images with the left and right hippocampus delineated into the head and body. We initialize the multi-atlas segmentation to a region directly around each lateralized hippocampus to both speed up and improve the accuracy of registration. This initialization allows for incorporation of nearly 200 atlases, an accomplishment which would typically involve hundreds of hours of computation per target image. The proposed segmentation results in a Dice similiarity coefficient over 0.9 for the full hippocampus. This result outperforms a multi-atlas segmentation using the BrainCOLOR atlases (Dice 0.85) and FreeSurfer (Dice 0.75). Furthermore, the head and body delineation resulted in a Dice coefficient over 0.87 for both structures. The head and body volume measurements also show high reproducibility on the Kirby 21 reproducibility population (R2 greater than 0.95, p develop a robust tool for measurement of the hippocampus and other temporal lobe structures.

  3. A unified framework for cross-modality multi-atlas segmentation of brain MRI

    DEFF Research Database (Denmark)

    Eugenio Iglesias, Juan; Rory Sabuncu, Mert; Van Leemput, Koen

    2013-01-01

    on the similarity of image intensities. Instead, it exploits the consistency of voxel intensities within the target scan to drive the registration and label fusion, hence the atlases and target image can be of different modalities. Furthermore, the framework models the joint warp of all the atlases, introducing...

  4. Test-retest assessment of cortical activation induced by repetitive transcranial magnetic stimulation with brain atlas-guided optical topography

    Science.gov (United States)

    Tian, Fenghua; Kozel, F. Andrew; Yennu, Amarnath; Croarkin, Paul E.; McClintock, Shawn M.; Mapes, Kimberly S.; Husain, Mustafa M.; Liu, Hanli

    2012-11-01

    Repetitive transcranial magnetic stimulation (rTMS) is a technology that stimulates neurons with rapidly changing magnetic pulses with demonstrated therapeutic applications for various neuropsychiatric disorders. Functional near-infrared spectroscopy (fNIRS) is a suitable tool to assess rTMS-evoked brain responses without interference from the magnetic or electric fields generated by the TMS coil. We have previously reported a channel-wise study of combined rTMS/fNIRS on the motor and prefrontal cortices, showing a robust decrease of oxygenated hemoglobin concentration (Δ[HbO2]) at the sites of 1-Hz rTMS and the contralateral brain regions. However, the reliability of this putative clinical tool is unknown. In this study, we develop a rapid optical topography approach to spatially characterize the rTMS-evoked hemodynamic responses on a standard brain atlas. A hemispherical approximation of the brain is employed to convert the three-dimensional topography on the complex brain surface to a two-dimensional topography in the spherical coordinate system. The test-retest reliability of the combined rTMS/fNIRS is assessed using repeated measurements performed two to three days apart. The results demonstrate that the Δ[HbO2] amplitudes have moderate-to-high reliability at the group level; and the spatial patterns of the topographic images have high reproducibility in size and a moderate degree of overlap at the individual level.

  5. Generation of Individual Whole-Brain Atlases With Resting-State fMRI Data Using Simultaneous Graph Computation and Parcellation.

    Science.gov (United States)

    Wang, J; Hao, Z; Wang, H

    2018-01-01

    The human brain can be characterized as functional networks. Therefore, it is important to subdivide the brain appropriately in order to construct reliable networks. Resting-state functional connectivity-based parcellation is a commonly used technique to fulfill this goal. Here we propose a novel individual subject-level parcellation approach based on whole-brain resting-state functional magnetic resonance imaging (fMRI) data. We first used a supervoxel method known as simple linear iterative clustering directly on resting-state fMRI time series to generate supervoxels, and then combined similar supervoxels to generate clusters using a clustering method known as graph-without-cut (GWC). The GWC approach incorporates spatial information and multiple features of the supervoxels by energy minimization, simultaneously yielding an optimal graph and brain parcellation. Meanwhile, it theoretically guarantees that the actual cluster number is exactly equal to the initialized cluster number. By comparing the results of the GWC approach and those of the random GWC approach, we demonstrated that GWC does not rely heavily on spatial structures, thus avoiding the challenges encountered in some previous whole-brain parcellation approaches. In addition, by comparing the GWC approach to two competing approaches, we showed that GWC achieved better parcellation performances in terms of different evaluation metrics. The proposed approach can be used to generate individualized brain atlases for applications related to cognition, development, aging, disease, personalized medicine, etc. The major source codes of this study have been made publicly available at https://github.com/yuzhounh/GWC.

  6. Concordance of Time-of-Flight MRA and Digital Subtraction Angiography in Adult Primary Central Nervous System Vasculitis.

    Science.gov (United States)

    de Boysson, H; Boulouis, G; Parienti, J-J; Touzé, E; Zuber, M; Arquizan, C; Dequatre, N; Detante, O; Bienvenu, B; Aouba, A; Guillevin, L; Pagnoux, C; Naggara, O

    2017-10-01

    3D-TOF-MRA and DSA are 2 available tools to demonstrate neurovascular involvement in primary central nervous system vasculitis. We aimed to compare the diagnostic concordance of vessel imaging using 3D-TOF-MRA and DSA in patients with primary central nervous system vasculitis. We retrospectively identified all patients included in the French primary central nervous system vasculitis cohort of 85 patients who underwent, at baseline, both intracranial 3D-TOF-MRA and DSA in an interval of no more than 2 weeks and before treatment initiation. Two neuroradiologists independently reviewed all 3D-TOF-MRA and DSA imaging. Brain vasculature was divided into 25 arterial segments. Concordance between 3D-TOF-MRA and DSA for the identification of arterial stenosis was assessed by the Cohen κ Index. Thirty-one patients met the inclusion criteria, including 20 imaged with a 1.5T MR unit and 11 with a 3T MR unit. Among the 25 patients (81%) with abnormal DSA findings, 24 demonstrated abnormal 3D-TOF-MRA findings, whereas all 6 remaining patients with normal DSA findings had normal 3D-TOF-MRA findings. In the per-segment analysis, concordance between 1.5T 3D-TOF-MRA and DSA was 0.82 (95% CI, 0.75-0.93), and between 3T 3D-TOF-MRA and DSA, it was 0.87 (95% CI, 0.78-0.91). 3D-TOF-MRA shows a high concordance with DSA in diagnostic performance when analyzing brain vasculature in patients with primary central nervous system vasculitis. In patients with negative 3T 3D-TOF-MRA findings, the added diagnostic value of DSA is limited. © 2017 by American Journal of Neuroradiology.

  7. [The brain in stereotaxic coordinates (a textbook for colleges)].

    Science.gov (United States)

    Budantsev, A Iu; Kisliuk, O S; Shul'govskiĭ, V V; Rykunov, D S; Iarkov, A V

    1993-01-01

    The present textbook is directed forward students of universities and medical colleges, young scientists and practicing doctors dealing with stereotaxic method. The Paxinos and Watson stereotaxic rat brain atlas (1982) is the basis of the textbook. The atlas has been transformed into computer educational program and seven laboratory works: insertion of the electrode into brain, microelectrophoresis, microinjection of drugs into brain, electrolytic destruction in the brain structures, local brain superfusion. The laboratory works are compiled so that they allow not only to study practical use of the stereotaxic method but to model simple problems involving stereotaxic surgery in the deep structures of brain. The textbook is intended for carrying by IBM PC/AT computers. The volume of the textbook is 1.7 Mbytes.

  8. Atlas-based delineation of lymph node levels in head and neck computed tomography images

    International Nuclear Information System (INIS)

    Commowick, Olivier; Gregoire, Vincent; Malandain, Gregoire

    2008-01-01

    Purpose: Radiotherapy planning requires accurate delineations of the tumor and of the critical structures. Atlas-based segmentation has been shown to be very efficient to automatically delineate brain critical structures. We therefore propose to construct an anatomical atlas of the head and neck region. Methods and materials: Due to the high anatomical variability of this region, an atlas built from a single image as for the brain is not adequate. We address this issue by building a symmetric atlas from a database of manually segmented images. First, we develop an atlas construction method and apply it to a database of 45 Computed Tomography (CT) images from patients with node-negative pharyngo-laryngeal squamous cell carcinoma manually delineated for radiotherapy. Then, we qualitatively and quantitatively evaluate the results generated by the built atlas based on Leave-One-Out framework on the database. Results: We present qualitative and quantitative results using this atlas construction method. The evaluation was performed on a subset of 12 patients among the original CT database of 45 patients. Qualitative results depict visually well delineated structures. The quantitative results are also good, with an error with respect to the best achievable results ranging from 0.196 to 0.404 with a mean of 0.253. Conclusions: These results show the feasibility of using such an atlas for radiotherapy planning. Many perspectives are raised from this work ranging from extensive validation to the construction of several atlases representing sub-populations, to account for large inter-patient variabilities, and populations with node-positive tumors

  9. In vivo quantitative whole-brain diffusion tensor imaging analysis of APP/PS1 transgenic mice using voxel-based and atlas-based methods

    International Nuclear Information System (INIS)

    Qin, Yuan-Yuan; Li, Mu-Wei; Oishi, Kenichi; Zhang, Shun; Zhang, Yan; Zhao, Ling-Yun; Zhu, Wen-Zhen; Lei, Hao

    2013-01-01

    Diffusion tensor imaging (DTI) has been applied to characterize the pathological features of Alzheimer's disease (AD) in a mouse model, although little is known about whether these features are structure specific. Voxel-based analysis (VBA) and atlas-based analysis (ABA) are good complementary tools for whole-brain DTI analysis. The purpose of this study was to identify the spatial localization of disease-related pathology in an AD mouse model. VBA and ABA quantification were used for the whole-brain DTI analysis of nine APP/PS1 mice and wild-type (WT) controls. Multiple scalar measurements, including fractional anisotropy (FA), trace, axial diffusivity (DA), and radial diffusivity (DR), were investigated to capture the various types of pathology. The accuracy of the image transformation applied for VBA and ABA was evaluated by comparing manual and atlas-based structure delineation using kappa statistics. Following the MR examination, the brains of the animals were analyzed for microscopy. Extensive anatomical alterations were identified in APP/PS1 mice, in both the gray matter areas (neocortex, hippocampus, caudate putamen, thalamus, hypothalamus, claustrum, amygdala, and piriform cortex) and the white matter areas (corpus callosum/external capsule, cingulum, septum, internal capsule, fimbria, and optic tract), evidenced by an increase in FA or DA, or both, compared to WT mice (p 0.05). The histopathological changes in the gray matter areas were confirmed by microscopy studies. DTI did, however, demonstrate significant changes in white matter areas, where the difference was not apparent by qualitative observation of a single-slice histological specimen. This study demonstrated the structure-specific nature of pathological changes in APP/PS1 mouse, and also showed the feasibility of applying whole-brain analysis methods to the investigation of an AD mouse model. (orig.)

  10. Consanguinity and spousal concordance in Kuwait.

    Science.gov (United States)

    al-Kandari, Y; Crews, D E; Poirier, F E

    2002-12-01

    Consanguineous marriage is favored in Kuwait. This research focuses on the relationship of physical and cultural traits to marriage types in Kuwait and examines concordance as a function of consanguinity and marriage duration. In a nonrandom opportunistic sample of 242 couples anthropometric and blood pressure data have been collected as well as data on acculturation, religiosity, Farsi proficiency, level of education, occupation, and attitudes regarding fertility. Significant concordances occur in cultural characteristics among couples in all three types of marriages with respect to the degree of religiosity, acculturation, language similarity, education, and occupation. Non-consanguineous spouses have the highest concordance in educational level, occupation, and degree of acculturation, but the lowest for religiosity and Farsi proficiency. Nonkin marriages seem to be based on personal preferences. In the wider potential nonkin marriage pool spouses show more concordance in stature and education indicating the positive assortative mating for those traits. Non-consanguineous spouses show a significant association for triceps and subscapular skinfold thicknesses hip and waist circumferences, and body fat distribution. Unrelated spouses exhibit more concordance for physical traits than do related spouses. There is a significant correlation between spouses in first and double cousin marriages as well as in spouses in second and less than second cousin unions for systolic and diastolic blood pressure, while non-consanguineous spouses show a significant association in diastolic blood pressure only.

  11. Robust Estimation of Electron Density From Anatomic Magnetic Resonance Imaging of the Brain Using a Unifying Multi-Atlas Approach

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Shangjie [Tianjin Key Laboratory of Process Measurement and Control, School of Electrical Engineering and Automation, Tianjin University, Tianjin (China); Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California (United States); Hara, Wendy; Wang, Lei; Buyyounouski, Mark K.; Le, Quynh-Thu; Xing, Lei [Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California (United States); Li, Ruijiang, E-mail: rli2@stanford.edu [Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, California (United States)

    2017-03-15

    Purpose: To develop a reliable method to estimate electron density based on anatomic magnetic resonance imaging (MRI) of the brain. Methods and Materials: We proposed a unifying multi-atlas approach for electron density estimation based on standard T1- and T2-weighted MRI. First, a composite atlas was constructed through a voxelwise matching process using multiple atlases, with the goal of mitigating effects of inherent anatomic variations between patients. Next we computed for each voxel 2 kinds of conditional probabilities: (1) electron density given its image intensity on T1- and T2-weighted MR images; and (2) electron density given its spatial location in a reference anatomy, obtained by deformable image registration. These were combined into a unifying posterior probability density function using the Bayesian formalism, which provided the optimal estimates for electron density. We evaluated the method on 10 patients using leave-one-patient-out cross-validation. Receiver operating characteristic analyses for detecting different tissue types were performed. Results: The proposed method significantly reduced the errors in electron density estimation, with a mean absolute Hounsfield unit error of 119, compared with 140 and 144 (P<.0001) using conventional T1-weighted intensity and geometry-based approaches, respectively. For detection of bony anatomy, the proposed method achieved an 89% area under the curve, 86% sensitivity, 88% specificity, and 90% accuracy, which improved upon intensity and geometry-based approaches (area under the curve: 79% and 80%, respectively). Conclusion: The proposed multi-atlas approach provides robust electron density estimation and bone detection based on anatomic MRI. If validated on a larger population, our work could enable the use of MRI as a primary modality for radiation treatment planning.

  12. An extensive assessment of network alignment algorithms for comparison of brain connectomes.

    Science.gov (United States)

    Milano, Marianna; Guzzi, Pietro Hiram; Tymofieva, Olga; Xu, Duan; Hess, Christofer; Veltri, Pierangelo; Cannataro, Mario

    2017-06-06

    Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. The atlas-based parcellations present some known limitations in cases of early brain development and abnormal anatomy. Consequently, it has been recently proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space, as a way to deal with the unknown correspondences of the parcels. Such process requires modeling of the brain using graph theory and the subsequent comparison of the structure of graphs. The latter step may be modeled as a network alignment (NA) problem. In this work, we first define the problem formally, then we test six existing state of the art of network aligners on diffusion MRI-derived brain networks. We compare the performances of algorithms by assessing six topological measures. We also evaluated the robustness of algorithms to alterations of the dataset. The results confirm that NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes. The analysis shows MAGNA++ is the best global alignment algorithm. The paper presented a new analysis methodology that uses network alignment for validating atlas-free parcellation brain connectomes. The methodology has been experimented on several brain datasets.

  13. Automated tissue classification of pediatric brains from magnetic resonance images using age-specific atlases

    Science.gov (United States)

    Metzger, Andrew; Benavides, Amanda; Nopoulos, Peg; Magnotta, Vincent

    2016-03-01

    The goal of this project was to develop two age appropriate atlases (neonatal and one year old) that account for the rapid growth and maturational changes that occur during early development. Tissue maps from this age group were initially created by manually correcting the resulting tissue maps after applying an expectation maximization (EM) algorithm and an adult atlas to pediatric subjects. The EM algorithm classified each voxel into one of ten possible tissue types including several subcortical structures. This was followed by a novel level set segmentation designed to improve differentiation between distal cortical gray matter and white matter. To minimize the req uired manual corrections, the adult atlas was registered to the pediatric scans using high -dimensional, symmetric image normalization (SyN) registration. The subject images were then mapped to an age specific atlas space, again using SyN registration, and the resulting transformation applied to the manually corrected tissue maps. The individual maps were averaged in the age specific atlas space and blurred to generate the age appropriate anatomical priors. The resulting anatomical priors were then used by the EM algorithm to re-segment the initial training set as well as an independent testing set. The results from the adult and age-specific anatomical priors were compared to the manually corrected results. The age appropriate atlas provided superior results as compared to the adult atlas. The image analysis pipeline used in this work was built using the open source software package BRAINSTools.

  14. An imaging atlas of human anatomy

    International Nuclear Information System (INIS)

    Weir, J.; Abrahams, P.H.

    1993-01-01

    The atlas presents pictures obtained by the various imaging techniques, showing the normal anatomy of the various body regions in healthy adults. The pictures are the major information given, accompanying texts are reduced to captions giving the Latin names of important anatomic details or a brief introduction each to the fundamental characteristics of the imaging methods used, as e.g. angiography, computerized tomography, magnetic resonance imaging, and ultrasonography. The atlas is a key source of reference and a guide in interpreting radiographs. The material is arranged in chapters according to the body regions of interest: Head, neck, brain; spine and spinal cord; upper extremities; thorax; abdomen; pelvis; lower extremities. (UWA) [de

  15. Workbench surface editor of brain cortical surface

    Science.gov (United States)

    Dow, Douglas E.; Nowinski, Wieslaw L.; Serra, Luis

    1996-04-01

    We have developed a 3D reach-in tool to manually reconstruct 3D cortical surface patches from 2D brain atlas images. The first application of our cortex editor is building 3D functional maps, specifically Brodmann's areas. This tool may also be useful in clinical practice to adjust incorrectly mapped atlas regions due to the deforming effect of lesions. The cortex editor allows a domain expert to control the correlation of control points across slices. Correct correlation has been difficult for 3D reconstruction algorithms because the atlas slices are far apart and because of the complex topology of the cortex which differs so much from slice to slice. Also, higher precision of the resulting surfaces is demanded since these define 3D brain atlas features upon which future stereotactic surgery may be based. The cortex editor described in this paper provides a tool suitable for a domain expert to use in defining the 3D surface of a Brodmann's area.

  16. Clinical Evaluation of Zero-Echo-Time Attenuation Correction for Brain 18F-FDG PET/MRI: Comparison with Atlas Attenuation Correction.

    Science.gov (United States)

    Sekine, Tetsuro; Ter Voert, Edwin E G W; Warnock, Geoffrey; Buck, Alfred; Huellner, Martin; Veit-Haibach, Patrick; Delso, Gaspar

    2016-12-01

    Accurate attenuation correction (AC) on PET/MR is still challenging. The purpose of this study was to evaluate the clinical feasibility of AC based on fast zero-echo-time (ZTE) MRI by comparing it with the default atlas-based AC on a clinical PET/MR scanner. We recruited 10 patients with malignant diseases not located on the brain. In all patients, a clinically indicated whole-body 18 F-FDG PET/CT scan was acquired. In addition, a head PET/MR scan was obtained voluntarily. For each patient, 2 AC maps were generated from the MR images. One was atlas-AC, derived from T1-weighted liver acquisition with volume acceleration flex images (clinical standard). The other was ZTE-AC, derived from proton-density-weighted ZTE images by applying tissue segmentation and assigning continuous attenuation values to the bone. The AC map generated by PET/CT was used as a silver standard. On the basis of each AC map, PET images were reconstructed from identical raw data on the PET/MR scanner. All PET images were normalized to the SPM5 PET template. After that, these images were qualified visually and quantified in 67 volumes of interest (VOIs; automated anatomic labeling, atlas). Relative differences and absolute relative differences between PET images based on each AC were calculated. 18 F-FDG uptake in all 670 VOIs and generalized merged VOIs were compared using a paired t test. Qualitative analysis shows that ZTE-AC was robust to patient variability. Nevertheless, misclassification of air and bone in mastoid and nasal areas led to the overestimation of PET in the temporal lobe and cerebellum (%diff of ZTE-AC, 2.46% ± 1.19% and 3.31% ± 1.70%, respectively). The |%diff| of all 670 VOIs on ZTE was improved by approximately 25% compared with atlas-AC (ZTE-AC vs. atlas-AC, 1.77% ± 1.41% vs. 2.44% ± 1.63%, P PET in regions near the skull base. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  17. Concorde Re-visited

    Science.gov (United States)

    Horton, Peter; Moore, Peter

    This year marks the twentieth anniversary of the introduction of Concorde into commercial airline service. The first commercial flights were on 21 January 1976 - British Airways from Heathrow to Bahrain and Air France from Paris to Rio via Dakar. Later in that year commercial flights to Washington/Dulles began on 24 May. Services to New York were delayed until 22 November 1977. The first flight of Concorde was some seven years earlier. The prototype took off out of Toulouse on 2 March 1969 and this was followed by 002 from Filton to Fairford on 9 April. At the time it was anticipated that this was the beginning of an era when supersonic flight would be the normal way to travel long distances. Now, in 1996, Concorde is still the world's only supersonic commercial passenger airliner in airline service. This is an extraordinary achievement. The Boeing SST proved to be too ambitious and the programme was halted in 1971 after the United States Government withdrew support, while the Russian TU 144 was beset with problems. One TU 144 crashed at the Paris Air Show in 1973. The aircraft entered internal airline service in December 1975, flying supersonically between Moscow and Alma-Ata, capital of Kazakhstan, carrying mail and freight, but it did not have the range to operate viable intercontinental passenger serives. Certainly by 1985, if not many years before, the TU 144 was out of service.

  18. TERRAIN, Concord, Massachusetts

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Concord AOI consists of one area. Ground Control is collected throughout the AOI for use in the processing of LiDAR data to ensure data accurately represents the...

  19. MRI-based treatment planning with pseudo CT generated through atlas registration

    International Nuclear Information System (INIS)

    Uh, Jinsoo; Merchant, Thomas E.; Hua, Chiaho; Li, Yimei; Li, Xingyu

    2014-01-01

    Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the

  20. MRI-based treatment planning with pseudo CT generated through atlas registration

    Energy Technology Data Exchange (ETDEWEB)

    Uh, Jinsoo, E-mail: jinsoo.uh@stjude.org; Merchant, Thomas E.; Hua, Chiaho [Department of Radiological Sciences, St. Jude Children' s Research Hospital, Memphis, Tennessee 38105 (United States); Li, Yimei; Li, Xingyu [Department of Biostatistics, St. Jude Children' s Research Hospital, Memphis, Tennessee 38105 (United States)

    2014-05-15

    Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787–0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%–98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the

  1. Generation of Individual Whole-Brain Atlases With Resting-State fMRI Data Using Simultaneous Graph Computation and Parcellation

    Directory of Open Access Journals (Sweden)

    J. Wang

    2018-05-01

    Full Text Available The human brain can be characterized as functional networks. Therefore, it is important to subdivide the brain appropriately in order to construct reliable networks. Resting-state functional connectivity-based parcellation is a commonly used technique to fulfill this goal. Here we propose a novel individual subject-level parcellation approach based on whole-brain resting-state functional magnetic resonance imaging (fMRI data. We first used a supervoxel method known as simple linear iterative clustering directly on resting-state fMRI time series to generate supervoxels, and then combined similar supervoxels to generate clusters using a clustering method known as graph-without-cut (GWC. The GWC approach incorporates spatial information and multiple features of the supervoxels by energy minimization, simultaneously yielding an optimal graph and brain parcellation. Meanwhile, it theoretically guarantees that the actual cluster number is exactly equal to the initialized cluster number. By comparing the results of the GWC approach and those of the random GWC approach, we demonstrated that GWC does not rely heavily on spatial structures, thus avoiding the challenges encountered in some previous whole-brain parcellation approaches. In addition, by comparing the GWC approach to two competing approaches, we showed that GWC achieved better parcellation performances in terms of different evaluation metrics. The proposed approach can be used to generate individualized brain atlases for applications related to cognition, development, aging, disease, personalized medicine, etc. The major source codes of this study have been made publicly available at https://github.com/yuzhounh/GWC.

  2. Patient-provider language concordance and colorectal cancer screening.

    Science.gov (United States)

    Linsky, Amy; McIntosh, Nathalie; Cabral, Howard; Kazis, Lewis E

    2011-02-01

    Patient-provider language barriers may play a role in health-care disparities, including obtaining colorectal cancer (CRC) screening. Professional interpreters and language-concordant providers may mitigate these disparities. DESIGN, SUBJECTS, AND MAIN MEASURES: We performed a retrospective cohort study of individuals age 50 years and older who were categorized as English-Concordant (spoke English at home, n = 21,594); Other Language-Concordant (did not speak English at home but someone at their provider's office spoke their language, n = 1,463); or Other Language-Discordant (did not speak English at home and no one at their provider's spoke their language, n = 240). Multivariate logistic regression assessed the association of language concordance with colorectal cancer screening. Compared to English speakers, non-English speakers had lower use of colorectal cancer screening (30.7% vs 50.8%; OR, 0.63; 95% CI, 0.51-0.76). Compared to the English-Concordant group, the Language-Discordant group had similar screening (adjusted OR, 0.84; 95% CI, 0.58-1.21), while the Language-Concordant group had lower screening (adjusted OR, 0.57; 95% CI, 0.46-0.71). Rates of CRC screening are lower in individuals who do not speak English at home compared to those who do. However, the Language-Discordant cohort had similar rates to those with English concordance, while the Language-Concordant cohort had lower rates of CRC screening. This may be due to unmeasured differences among the cohorts in patient, provider, and health care system characteristics. These results suggest that providers should especially promote the importance of CRC screening to non-English speaking patients, but that language barriers do not fully account for CRC screening rate disparities in these populations.

  3. Disease-Concordant Twins Empower Genetic Association Studies

    DEFF Research Database (Denmark)

    Tan, Qihua; Li, Weilong; Vandin, Fabio

    2017-01-01

    and ordinary healthy samples as controls. We examined the power gain of the twin-based design for various scenarios (i.e., cases from monozygotic and dizygotic twin pairs concordant for a disease) and compared the power with the ordinary case-control design with cases collected from the unrelated patient...... concordant for a disease, should confer increased power in genetic association analysis because of their genetic relatedness. We conducted a computer simulation study to explore the power advantage of the disease-concordant twin design, which uses singletons from disease-concordant twin pairs as cases...... population. Simulation was done by assigning various allele frequencies and allelic relative risks for different mode of genetic inheritance. In general, for achieving a power estimate of 80%, the sample sizes needed for dizygotic and monozygotic twin cases were one half and one fourth of the sample size...

  4. An atlas-based multimodal registration method for 2D images with discrepancy structures.

    Science.gov (United States)

    Lv, Wenchao; Chen, Houjin; Peng, Yahui; Li, Yanfeng; Li, Jupeng

    2018-06-04

    An atlas-based multimodal registration method for 2-dimension images with discrepancy structures was proposed in this paper. Atlas was utilized for complementing the discrepancy structure information in multimodal medical images. The scheme includes three steps: floating image to atlas registration, atlas to reference image registration, and field-based deformation. To evaluate the performance, a frame model, a brain model, and clinical images were employed in registration experiments. We measured the registration performance by the squared sum of intensity differences. Results indicate that this method is robust and performs better than the direct registration for multimodal images with discrepancy structures. We conclude that the proposed method is suitable for multimodal images with discrepancy structures. Graphical Abstract An Atlas-based multimodal registration method schematic diagram.

  5. Creation of computerized 3D MRI-integrated atlases of the human basal ganglia and thalamus

    Directory of Open Access Journals (Sweden)

    Abbas F. Sadikot

    2011-09-01

    Full Text Available Functional brain imaging and neurosurgery in subcortical areas often requires visualization of brain nuclei beyond the resolution of current Magnetic Resonance Imaging (MRI methods. We present techniques used to create: 1 a lower resolution 3D atlas, based on the Schaltenbrand and Wahren print atlas, which was integrated into a stereotactic neurosurgery planning and visualization platform (VIPER; and 2 a higher resolution 3D atlas derived from a single set of manually segmented histological slices containing nuclei of the basal ganglia, thalamus, basal forebrain and medial temporal lobe. Both atlases were integrated to a canonical MRI (Colin27 from a young male participant by manually identifying homologous landmarks. The lower resolution atlas was then warped to fit the MRI based on the identified landmarks. A pseudo-MRI representation of the high-resolution atlas was created, and a nonlinear transformation was calculated in order to match the atlas to the template MRI. The atlas can then be warped to match the anatomy of Parkinson’s disease surgical candidates by using 3D automated nonlinear deformation methods. By way of functional validation of the atlas, the location of the sensory thalamus was correlated with stereotactic intraoperative physiological data. The position of subthalamic electrode positions in patients with Parkinson’s disease was also evaluated in the atlas-integrated MRI space. Finally, probabilistic maps of subthalamic stimulation electrodes were developed, in order to allow group analysis of the location of contacts associated with the best motor outcomes. We have therefore developed, and are continuing to validate, a high-resolution computerized MRI-integrated 3D histological atlas, which is useful in functional neurosurgery, and for functional and anatomical studies of the human basal ganglia, thalamus and basal forebrain.

  6. Moderators of Implicit-Explicit Exercise Cognition Concordance.

    Science.gov (United States)

    Berry, Tanya R; Rodgers, Wendy M; Markland, David; Hall, Craig R

    2016-12-01

    Investigating implicit-explicit concordance can aid in understanding underlying mechanisms and possible intervention effects. This research examined the concordance between implicit associations of exercise with health or appearance and related explicit motives. Variables considered as possible moderators were behavioral regulations, explicit attitudes, and social desirability. Participants (N = 454) completed measures of implicit associations of exercise with health and appearance and questionnaire measures of health and appearance motives, attitudes, social desirability, and behavioral regulations. Attitudes significantly moderated the relationship between implicit associations of exercise with health and health motives. Identified regulations significantly moderated implicit-explicit concordance with respect to associations with appearance. These results suggest that implicit and explicit exercise-related cognitions are not necessarily independent and their relationship to each other may be moderated by attitudes or some forms of behavioral regulation. Future research that takes a dual-processing approach to exercise behavior should consider potential theoretical moderators of concordance.

  7. TU-AB-202-10: How Effective Are Current Atlas Selection Methods for Atlas-Based Auto-Contouring in Radiotherapy Planning?

    Energy Technology Data Exchange (ETDEWEB)

    Peressutti, D; Schipaanboord, B; Kadir, T; Gooding, M [Mirada Medical Limited, Science and Medical Technology, Oxford (United Kingdom); Soest, J van; Lustberg, T; Elmpt, W van; Dekker, A [Maastricht University Medical Centre, Department of Radiation Oncology MAASTRO - GROW School for Oncology Developmental Biology, Maastricht (Netherlands)

    2016-06-15

    Purpose: To investigate the effectiveness of atlas selection methods for improving atlas-based auto-contouring in radiotherapy planning. Methods: 275 H&N clinically delineated cases were employed as an atlas database from which atlases would be selected. A further 40 previously contoured cases were used as test patients against which atlas selection could be performed and evaluated. 26 variations of selection methods proposed in the literature and used in commercial systems were investigated. Atlas selection methods comprised either global or local image similarity measures, computed after rigid or deformable registration, combined with direct atlas search or with an intermediate template image. Workflow Box (Mirada-Medical, Oxford, UK) was used for all auto-contouring. Results on brain, brainstem, parotids and spinal cord were compared to random selection, a fixed set of 10 “good” atlases, and optimal selection by an “oracle” with knowledge of the ground truth. The Dice score and the average ranking with respect to the “oracle” were employed to assess the performance of the top 10 atlases selected by each method. Results: The fixed set of “good” atlases outperformed all of the atlas-patient image similarity-based selection methods (mean Dice 0.715 c.f. 0.603 to 0.677). In general, methods based on exhaustive comparison of local similarity measures showed better average Dice scores (0.658 to 0.677) compared to the use of either template image (0.655 to 0.672) or global similarity measures (0.603 to 0.666). The performance of image-based selection methods was found to be only slightly better than a random (0.645). Dice scores given relate to the left parotid, but similar results patterns were observed for all organs. Conclusion: Intuitively, atlas selection based on the patient CT is expected to improve auto-contouring performance. However, it was found that published approaches performed marginally better than random and use of a fixed set of

  8. Sensitivity analysis of human brain structural network construction

    Directory of Open Access Journals (Sweden)

    Kuang Wei

    2017-12-01

    Full Text Available Network neuroscience leverages diffusion-weighted magnetic resonance imaging and tractography to quantify structural connectivity of the human brain. However, scientists and practitioners lack a clear understanding of the effects of varying tractography parameters on the constructed structural networks. With diffusion images from the Human Connectome Project (HCP, we characterize how structural networks are impacted by the spatial resolution of brain atlases, total number of tractography streamlines, and grey matter dilation with various graph metrics. We demonstrate how injudicious combinations of highly refined brain parcellations and low numbers of streamlines may inadvertently lead to disconnected network models with isolated nodes. Furthermore, we provide solutions to significantly reduce the likelihood of generating disconnected networks. In addition, for different tractography parameters, we investigate the distributions of values taken by various graph metrics across the population of HCP subjects. Analyzing the ranks of individual subjects within the graph metric distributions, we find that the ranks of individuals are affected differently by atlas scale changes. Our work serves as a guideline for researchers to optimize the selection of tractography parameters and illustrates how biological characteristics of the brain derived in network neuroscience studies can be affected by the choice of atlas parcellation schemes. Diffusion tractography has been proven to be a promising noninvasive technique to study the network properties of the human brain. However, how various tractography and network construction parameters affect network properties has not been studied using a large cohort of high-quality data. We utilize data provided by the Human Connectome Project to characterize the changes to network properties induced by varying the brain parcellation atlas scales, the number of reconstructed tractography tracks, and the degree of grey

  9. Concordance for prognostic models with competing risks

    DEFF Research Database (Denmark)

    Wolbers, Marcel; Blanche, Paul; Koller, Michael T

    2014-01-01

    The concordance probability is a widely used measure to assess discrimination of prognostic models with binary and survival endpoints. We formally define the concordance probability for a prognostic model of the absolute risk of an event of interest in the presence of competing risks and relate i...

  10. Civic Friendship in Aristotle: Concord and Fraternity

    Directory of Open Access Journals (Sweden)

    Oriol Farrés Juste

    2015-05-01

    Full Text Available the article shows the importance of friendship in the context of Aristotelian political philosophy. this importance is verified in its specific weight compared with justice. As it is known, Aristotle argues that the pursuit of friendship outranks the pursuit of justice in the polis. Particularly, the article focuses on the role of concord, as a special type of civic friendship, in terms of preserving the unity and stability of the polis. to grasp its significance, we have to consider the role of concord as a supplement of the political condition of the human being. Concord is necessary in the light of the trend to the struggle between the parts of the city, between the demos and the oligarchs. Since this fight endangers the continuity of the polis, concord among citizens becomes a privileged background of early republican fraternity, which has not enjoyed sufficient attention in the field of history of political philosophy.

  11. Bayesian estimation of regularization and atlas building in diffeomorphic image registration.

    Science.gov (United States)

    Zhang, Miaomiao; Singh, Nikhil; Fletcher, P Thomas

    2013-01-01

    This paper presents a generative Bayesian model for diffeomorphic image registration and atlas building. We develop an atlas estimation procedure that simultaneously estimates the parameters controlling the smoothness of the diffeomorphic transformations. To achieve this, we introduce a Monte Carlo Expectation Maximization algorithm, where the expectation step is approximated via Hamiltonian Monte Carlo sampling on the manifold of diffeomorphisms. An added benefit of this stochastic approach is that it can successfully solve difficult registration problems involving large deformations, where direct geodesic optimization fails. Using synthetic data generated from the forward model with known parameters, we demonstrate the ability of our model to successfully recover the atlas and regularization parameters. We also demonstrate the effectiveness of the proposed method in the atlas estimation problem for 3D brain images.

  12. Three-dimensional stereotactic atlas of the extracranial vasculature correlated with the intracranial vasculature, cranial nerves, skull and muscles.

    Science.gov (United States)

    Nowinski, Wieslaw L; Shoon Let Thaung, Thant; Choon Chua, Beng; Hnin Wut Yi, Su; Yang, Yili; Urbanik, Andrzej

    2015-04-01

    Our objective was to construct a 3D, interactive, and reference atlas of the extracranial vasculature spatially correlated with the intracranial blood vessels, cranial nerves, skull, glands, and head muscles.The atlas has been constructed from multiple 3T and 7T magnetic resonance angiogram (MRA) brain scans, and 3T phase contrast and inflow MRA neck scans of the same specimen in the following steps: vessel extraction from the scans, building 3D tubular models of the vessels, spatial registration of the extra- and intracranial vessels, vessel editing, vessel naming and color-coding, vessel simplification, and atlas validation.This new atlas contains 48 names of the extracranial vessels (25 arterial and 23 venous) and it has been integrated with the existing brain atlas.The atlas is valuable for medical students and residents to easily get familiarized with the extracranial vasculature with a few clicks; is useful for educators to prepare teaching materials; and potentially can serve as a reference in the diagnosis of vascular disease and treatment, including craniomaxillofacial surgeries and radiologic interventions of the face and neck. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  13. Recent Development in the ATLAS Control Room

    CERN Document Server

    Armen Vartapetian

    Only recently the name ATLAS Control Room (ACR) was more associated with the building at Point 1 (SCX1) than with the real thing. But just within the last several months, with the installation of the ACR hardware, that perception has changed significantly. The recently furnished ATLAS control room. But first of all, if you are not familiar with the ATLAS experimental site and are interested in visiting the ATLAS control room to see the place that in the near future will become the brain of the detector operations, it is quite easy to do so. You don't even need safety helmet or shoes! The ACR is located on the ground floor of a not so typical, glass-covered building in Point 1. The building number on the CERN map is 3162, or SCX1 as we call it. It is also easy to recognize that building by its shiny appearance within the cluster of Point 1 buildings if you are driving from Geneva. Final design and prototyping of the ACR hardware started at the beginning of 2006. Evaluation of the chosen hardware confi...

  14. Unifying framework for multimodal brain MRI segmentation based on Hidden Markov Chains.

    Science.gov (United States)

    Bricq, S; Collet, Ch; Armspach, J P

    2008-12-01

    In the frame of 3D medical imaging, accurate segmentation of multimodal brain MR images is of interest for many brain disorders. However, due to several factors such as noise, imaging artifacts, intrinsic tissue variation and partial volume effects, tissue classification remains a challenging task. In this paper, we present a unifying framework for unsupervised segmentation of multimodal brain MR images including partial volume effect, bias field correction, and information given by a probabilistic atlas. Here-proposed method takes into account neighborhood information using a Hidden Markov Chain (HMC) model. Due to the limited resolution of imaging devices, voxels may be composed of a mixture of different tissue types, this partial volume effect is included to achieve an accurate segmentation of brain tissues. Instead of assigning each voxel to a single tissue class (i.e., hard classification), we compute the relative amount of each pure tissue class in each voxel (mixture estimation). Further, a bias field estimation step is added to the proposed algorithm to correct intensity inhomogeneities. Furthermore, atlas priors were incorporated using probabilistic brain atlas containing prior expectations about the spatial localization of different tissue classes. This atlas is considered as a complementary sensor and the proposed method is extended to multimodal brain MRI without any user-tunable parameter (unsupervised algorithm). To validate this new unifying framework, we present experimental results on both synthetic and real brain images, for which the ground truth is available. Comparison with other often used techniques demonstrates the accuracy and the robustness of this new Markovian segmentation scheme.

  15. Behavioral and neural concordance in parent-child dyadic sleep patterns.

    Science.gov (United States)

    Lee, Tae-Ho; Miernicki, Michelle E; Telzer, Eva H

    2017-08-01

    Sleep habits developed in adolescence shape long-term trajectories of psychological, educational, and physiological well-being. Adolescents' sleep behaviors are shaped by their parents' sleep at both the behavioral and biological levels. In the current study, we sought to examine how neural concordance in resting-state functional connectivity between parent-child dyads is associated with dyadic concordance in sleep duration and adolescents' sleep quality. To this end, we scanned both parents and their child (N=28 parent-child dyads; parent M age =42.8years; adolescent M age =14.9years; 14.3% father; 46.4% female adolescent) as they each underwent a resting-state scan. Using daily diaries, we also assessed dyadic concordance in sleep duration across two weeks. Our results show that greater daily concordance in sleep behavior is associated with greater neural concordance in default-mode network connectivity between parents and children. Moreover, greater neural and behavioral concordances in sleep is associated with more optimal sleep quality in adolescents. The current findings expand our understanding of dyadic concordance by providing a neurobiological mechanism by which parents and children share daily sleep behaviors. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Estimating twin concordance for bivariate competing risks twin data

    DEFF Research Database (Denmark)

    Scheike, Thomas; Holst, Klaus K.; Hjelmborg, Jacob B.

    2014-01-01

    For twin time-to-event data, we consider different concordance probabilities, such as the casewise concordance that are routinely computed as a measure of the lifetime dependence/correlation for specific diseases. The concordance probability here is the probability that both twins have experience...... events with the competing risk death. We thus aim to quantify the degree of dependence through the casewise concordance function and show a significant genetic component...... the event of interest. Under the assumption that both twins are censored at the same time, we show how to estimate this probability in the presence of right censoring, and as a consequence, we can then estimate the casewise twin concordance. In addition, we can model the magnitude of within pair dependence...... over time, and covariates may be further influential on the marginal risk and dependence structure. We establish the estimators large sample properties and suggest various tests, for example, for inferring familial influence. The method is demonstrated and motivated by specific twin data on cancer...

  17. Models and methods of emotional concordance.

    Science.gov (United States)

    Hollenstein, Tom; Lanteigne, Dianna

    2014-04-01

    Theories of emotion generally posit the synchronized, coordinated, and/or emergent combination of psychophysiological, cognitive, and behavioral components of the emotion system--emotional concordance--as a functional definition of emotion. However, the empirical support for this claim has been weak or inconsistent. As an introduction to this special issue on emotional concordance, we consider three domains of explanations as to why this theory-data gap might exist. First, theory may need to be revised to more accurately reflect past research. Second, there may be moderating factors such as emotion regulation, context, or individual differences that have obscured concordance. Finally, the methods typically used to test theory may be inadequate. In particular, we review a variety of potential issues: intensity of emotions elicited in the laboratory, nonlinearity, between- versus within-subject associations, the relative timing of components, bivariate versus multivariate approaches, and diversity of physiological processes. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Mapping neuroplastic potential in brain-damaged patients.

    Science.gov (United States)

    Herbet, Guillaume; Maheu, Maxime; Costi, Emanuele; Lafargue, Gilles; Duffau, Hugues

    2016-03-01

    It is increasingly acknowledged that the brain is highly plastic. However, the anatomic factors governing the potential for neuroplasticity have hardly been investigated. To bridge this knowledge gap, we generated a probabilistic atlas of functional plasticity derived from both anatomic magnetic resonance imaging results and intraoperative mapping data on 231 patients having undergone surgery for diffuse, low-grade glioma. The atlas includes detailed level of confidence information and is supplemented with a series of comprehensive, connectivity-based cluster analyses. Our results show that cortical plasticity is generally high in the cortex (except in primary unimodal areas and in a small set of neural hubs) and rather low in connective tracts (especially associative and projection tracts). The atlas sheds new light on the topological organization of critical neural systems and may also be useful in predicting the likelihood of recovery (as a function of lesion topology) in various neuropathological conditions-a crucial factor in improving the care of brain-damaged patients. © The Author (2016). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Direct estimation of patient attributes from anatomical MRI based on multi-atlas voting

    Directory of Open Access Journals (Sweden)

    Dan Wu

    2016-01-01

    Full Text Available MRI brain atlases are widely used for automated image segmentation, and in particular, recent developments in multi-atlas techniques have shown highly accurate segmentation results. In this study, we extended the role of the atlas library from mere anatomical reference to a comprehensive knowledge database with various patient attributes, such as demographic, functional, and diagnostic information. In addition to using the selected (heavily-weighted atlases to achieve high segmentation accuracy, we tested whether the non-anatomical attributes of the selected atlases could be used to estimate patient attributes. This can be considered a context-based image retrieval (CBIR approach, embedded in the multi-atlas framework. We first developed an image similarity measurement to weigh the atlases on a structure-by-structure basis, and then, the attributes of the multiple atlases were weighted to estimate the patient attributes. We tested this concept first by estimating age in a normal population; we then performed functional and diagnostic estimations in Alzheimer's disease patients. The accuracy of the estimated patient attributes was measured against the actual clinical data, and the performance was compared to conventional volumetric analysis. The proposed CBIR framework by multi-atlas voting would be the first step toward a knowledge-based support system for quantitative radiological image reading and diagnosis.

  20. Direct estimation of patient attributes from anatomical MRI based on multi-atlas voting.

    Science.gov (United States)

    Wu, Dan; Ceritoglu, Can; Miller, Michael I; Mori, Susumu

    MRI brain atlases are widely used for automated image segmentation, and in particular, recent developments in multi-atlas techniques have shown highly accurate segmentation results. In this study, we extended the role of the atlas library from mere anatomical reference to a comprehensive knowledge database with various patient attributes, such as demographic, functional, and diagnostic information. In addition to using the selected (heavily-weighted) atlases to achieve high segmentation accuracy, we tested whether the non-anatomical attributes of the selected atlases could be used to estimate patient attributes. This can be considered a context-based image retrieval (CBIR) approach, embedded in the multi-atlas framework. We first developed an image similarity measurement to weigh the atlases on a structure-by-structure basis, and then, the attributes of the multiple atlases were weighted to estimate the patient attributes. We tested this concept first by estimating age in a normal population; we then performed functional and diagnostic estimations in Alzheimer's disease patients. The accuracy of the estimated patient attributes was measured against the actual clinical data, and the performance was compared to conventional volumetric analysis. The proposed CBIR framework by multi-atlas voting would be the first step toward a knowledge-based support system for quantitative radiological image reading and diagnosis.

  1. Estimating Twin Pair Concordance for Age of Onset

    DEFF Research Database (Denmark)

    Scheike, Thomas H; Hjelmborg, Jacob B; Holst, Klaus K

    2015-01-01

    that they will develop the disease. The aim of this contribution is to show that the standard casewise concordance and standard prevalence estimators do not work in general for age-of-onset data. We show how one can in fact do something easy and simple even with censored data. The key is to take age into account when......Twin and family data provide a key source for evaluating inheritance of specific diseases. A standard analysis of such data typically involves the computation of prevalences and different concordance measures such as the casewise concordance, that is the probability that one twin has the disease...

  2. Effect of cocaine on structural changes in brain: MRI volumetry using tensor-based morphometry.

    Science.gov (United States)

    Narayana, Ponnada A; Datta, Sushmita; Tao, Guozhi; Steinberg, Joel L; Moeller, F Gerard

    2010-10-01

    Magnetic resonance imaging (MRI) was performed in cocaine-dependent subjects to determine the structural changes in brain compared to non-drug using controls. Cocaine-dependent subjects and controls were carefully screened to rule out brain pathology of undetermined origin. Magnetic resonance images were analyzed using tensor-based morphometry (TBM) and voxel-based morphometry (VBM) without and with modulation to adjust for volume changes during normalization. For TBM analysis, unbiased atlases were generated using two different inverse consistent and diffeomorphic nonlinear registration techniques. Two different control groups were used for generating unbiased atlases. Independent of the nonlinear registration technique and normal cohorts used for creating the unbiased atlases, our analysis failed to detect any statistically significant effect of cocaine on brain volumes. These results show that cocaine-dependent subjects do not show differences in regional brain volumes compared to non-drug using controls. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  3. A valoração de traços de concordância dentro do DP Concord features valuing within DP

    Directory of Open Access Journals (Sweden)

    Telma M.V. Magalhães

    2004-06-01

    Full Text Available Este trabalho argumenta em favor da valoração dos traços de concordância dentro do DP em termos da operação Agree (Chomsky, 1999 sem a necessidade de estipular nenhum outro mecanismo para tanto. Mostro que Agree dá conta da valoração de traços tanto no nível da sentença quanto no nível do DP, contra a sugestão de Chomsky (1999 de que concordância no DP envolveria algum outro mecanismo de checagem.This paper argues in favor of a concord features valuing within the DP in terms of the Agree operation (Chomsky, 1999, with no recourse to any other mechanism. I show that Agree accounts for feature valuing both in the sentence level as well as in the DP, contrary to Chomsky's (1999 suggestion that concord in DP should involve some other checking mechanism.

  4. Assessing clinical reasoning in optometry using the script concordance test.

    Science.gov (United States)

    Faucher, Caroline; Dufour-Guindon, Marie-Pier; Lapointe, Gabrielle; Gagnon, Robert; Charlin, Bernard

    2016-05-01

    Clinical reasoning is central to any health profession but its development among learners is difficult to assess. Over the last few decades, the script concordance test (SCT) has been developed to solve this dilemma and has been used in many health professions; however, no study has been published on the use of the script concordance test in optometry. The purpose of this study was to develop and validate a script concordance test for the field of optometry. A 101-question script concordance test (27 short clinical scenarios) was developed and administered online to a convenience sample of 23 second-year and 19 fourth-year students of optometry. It was also administered to a reference panel of 12 experienced optometrists to develop the scoring key. An item-total correlation was calculated for each question. Cronbach's alpha coefficient was used to evaluate the script concordance test reliability and a t-test compared the two groups. A final 77-question script concordance test was created by eliminating questions with low item-total correlation. Cronbach's alpha for this optimised 77-question script concordance test was 0.80. A group comparison revealed that the second-year students' scores (n = 23; mean score = 66.4 ± 7.87 per cent) were statistically lower (t = -4.141; p Optometry © 2016 Optometry Australia.

  5. Methods for processing and analysis functional and anatomical brain images: computerized tomography, emission tomography and nuclear resonance imaging

    International Nuclear Information System (INIS)

    Mazoyer, B.M.

    1988-01-01

    The various methods for brain image processing and analysis are presented and compared. The following topics are developed: the physical basis of brain image comparison (nature and formation of signals intrinsic performance of the methods image characteristics); mathematical methods for image processing and analysis (filtering, functional parameter extraction, morphological analysis, robotics and artificial intelligence); methods for anatomical localization (neuro-anatomy atlas, proportional stereotaxic atlas, numerized atlas); methodology of cerebral image superposition (normalization, retiming); image networks [fr

  6. Atlas of fetal sectional anatomy with ultrasound and magnetic resonance imaging

    International Nuclear Information System (INIS)

    Isaacson, G.; Mintz, M.C.; Crelin, E.S.

    1986-01-01

    Here is an atlas of sectional anatomy for the fetus featuring correlated anatomy and imaging, transverse coronal and sagittal views, a guide to development of the brain, cardiac anatomy in standard plans of study and, over 280 illustrations

  7. Are physicians and patients in agreement? Exploring dyadic concordance.

    Science.gov (United States)

    Coran, Justin J; Koropeckyj-Cox, Tanya; Arnold, Christa L

    2013-10-01

    Dyadic concordance in physician-patient interactions can be defined as the extent of agreement between physicians and patients in their perceptions of the clinical encounter. The current research specifically examined two types of concordance: informational concordance-the extent of agreement in physician and patient responses regarding patient information (education, self-rated health, pain); and interactional concordance-the extent of physician-patient agreement regarding the patient's level of confidence and trust in the physician and the perceived quality of explanations concerning diagnosis and treatment. Using a convenience sample of physicians and patients (N = 50 dyads), a paired survey method was tested, which measured and compared physician and patient reports to identify informational and interactional concordances. Factors potentially related to dyadic concordance were also measured, including demographic characteristics (patient race, gender, age, and education) and clinical factors (whether this was a first visit and physician specialty in family medicine or oncology). The paired survey showed informational discordances, as physicians tended to underestimate patients' pain and overestimate patient education. Interactional discordances included overestimating patients' understanding of diagnosis and treatment explanations and patients' level of confidence and trust. Discordances were linked to patient dissatisfaction with physician listening, having unanswered questions, and feeling the physician had not spent enough time. The paired survey method effectively identified physician-patient discordances that may interfere with effective medical practice; this method may be used in various settings to identify potential areas of improvement in health communication and education.

  8. Quantification of Brain Access of Exendin-4 in the C57BL Mouse Model by SPIM Fluorescence Imaging and the Allen Mouse Brain Reference Model

    DEFF Research Database (Denmark)

    Jensen, Casper Bo; Secher, Anna; Hecksher-Sørensen, Jacob

    2015-01-01

    -4, into the brain with the aim of developing medication for obesity. To investigate mode of action of the medication it is important to identify the specific anatomical brain nuclei that are targeted by the compound. Such segmentations can be obtained using an annotated digital brain atlas. We...

  9. Concordance between clinical and histopathologic diagnoses of oral mucosal lesions.

    Science.gov (United States)

    Patel, Kush J; De Silva, Harsha L; Tong, Darryl C; Love, Robert M

    2011-01-01

    To study the epidemiology of oral soft tissue lesions in New Zealand from 2002 to 2006 and to determine the concordance between the clinical diagnosis and the definitive histopathologic diagnosis achieved by general dental practitioners and by specialists. The details from biopsy referrals and the corresponding histopathologic reports of oral soft tissue lesions were recorded into a statistical software package, and the concordance between the clinical diagnosis and histopathologic diagnosis was determined for all the lesions. Most biopsies were benign lesions, and both clinician groups achieved a high diagnostic concordance for these lesions. However, when considering all lesion types, the overall concordance for both groups was a moderate 50.6%, with little difference between specialists and general dental practitioners, although specialists were more accurate in diagnosing a malignant or premalignant lesion. The clinical and histopathologic concordance achieved by oral health practitioners in New Zealand appears to be moderate. Copyright © 2011 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

  10. A probabilistic atlas of the basal ganglia using 7 T MRI

    NARCIS (Netherlands)

    Keuken, M.C.; Forstmann, B.U.

    2015-01-01

    A common localization procedure in functional imaging studies includes the overlay of statistical parametric functional magnetic resonance imaging (fMRI) maps or coordinates with neuroanatomical atlases in standard space, e.g., MNI-space. This procedure allows the identification of specific brain

  11. Atlas-based identification of targets for functional radiosurgery

    International Nuclear Information System (INIS)

    Stancanello, Joseph; Romanelli, Pantaleo; Modugno, Nicola; Cerveri, Pietro; Ferrigno, Giancarlo; Uggeri, Fulvio; Cantore, Giampaolo

    2006-01-01

    Functional disorders of the brain, such as Parkinson's disease, dystonia, epilepsy, and neuropathic pain, may exhibit poor response to medical therapy. In such cases, surgical intervention may become necessary. Modern surgical approaches to such disorders include radio-frequency lesioning and deep brain stimulation (DBS). The subthalamic nucleus (STN) is one of the most useful stereotactic targets available: STN DBS is known to induce substantial improvement in patients with end-stage Parkinson's disease. Other targets include the Globus Pallidus pars interna (GPi) for dystonia and Parkinson's disease, and the centromedian nucleus of the thalamus (CMN) for neuropathic pain. Radiosurgery is an attractive noninvasive alternative to treat some functional brain disorders. The main technical limitation to radiosurgery is that the target can be selected only on the basis of magnetic resonance anatomy without electrophysiological confirmation. The aim of this work is to provide a method for the correct atlas-based identification of the target to be used in functional neurosurgery treatment planning. The coordinates of STN, CMN, and GPi were identified in the Talairach and Tournoux atlas and transformed to the corresponding regions of the Montreal Neurological Institute (MNI) electronic atlas. Binary masks describing the target nuclei were created. The MNI electronic atlas was deformed onto the patient magnetic resonance imaging-T1 scan by applying an affine transformation followed by a local nonrigid registration. The first transformation was based on normalized cross correlation and the second on optimization of a two-part objective function consisting of similarity criteria and weighted regularization. The obtained deformation field was then applied to the target masks. The minimum distance between the surface of an implanted electrode and the surface of the deformed mask was calculated. The validation of the method consisted of comparing the electrode-mask distance to

  12. Prediction future asset price which is non-concordant with the historical distribution

    Science.gov (United States)

    Seong, Ng Yew; Hin, Pooi Ah

    2015-12-01

    This paper attempts to predict the major characteristics of the future asset price which is non-concordant with the distribution estimated from the price today and the prices on a large number of previous days. The three major characteristics of the i-th non-concordant asset price are the length of the interval between the occurrence time of the previous non-concordant asset price and that of the present non-concordant asset price, the indicator which denotes that the non-concordant price is extremely small or large by its values -1 and 1 respectively, and the degree of non-concordance given by the negative logarithm of the probability of the left tail or right tail of which one of the end points is given by the observed future price. The vector of three major characteristics of the next non-concordant price is modelled to be dependent on the vectors corresponding to the present and l - 1 previous non-concordant prices via a 3-dimensional conditional distribution which is derived from a 3(l + 1)-dimensional power-normal mixture distribution. The marginal distribution for each of the three major characteristics can then be derived from the conditional distribution. The mean of the j-th marginal distribution is an estimate of the value of the j-th characteristics of the next non-concordant price. Meanwhile, the 100(α/2) % and 100(1 - α/2) % points of the j-th marginal distribution can be used to form a prediction interval for the j-th characteristic of the next non-concordant price. The performance measures of the above estimates and prediction intervals indicate that the fitted conditional distribution is satisfactory. Thus the incorporation of the distribution of the characteristics of the next non-concordant price in the model for asset price has a good potential of yielding a more realistic model.

  13. Atlas-free surface reconstruction of the cortical grey-white interface in infants.

    Directory of Open Access Journals (Sweden)

    François Leroy

    Full Text Available BACKGROUND: The segmentation of the cortical interface between grey and white matter in magnetic resonance images (MRI is highly challenging during the first post-natal year. First, the heterogeneous brain maturation creates important intensity fluctuations across regions. Second, the cortical ribbon is highly folded creating complex shapes. Finally, the low tissue contrast and partial volume effects hamper cortex edge detection in parts of the brain. METHODS AND FINDINGS: We present an atlas-free method for segmenting the grey-white matter interface of infant brains in T2-weighted (T2w images. We used a broad characterization of tissue using features based not only on local contrast but also on geometric properties. Furthermore, inaccuracies in localization were reduced by the convergence of two evolving surfaces located on each side of the inner cortical surface. Our method has been applied to eleven brains of one- to four-month-old infants. Both quantitative validations against manual segmentations and sulcal landmarks demonstrated good performance for infants younger than two months old. Inaccuracies in surface reconstruction increased with age in specific brain regions where the tissue contrast decreased with maturation, such as in the central region. CONCLUSIONS: We presented a new segmentation method which achieved good to very good performance at the grey-white matter interface depending on the infant age. This method should reduce manual intervention and could be applied to pathological brains since it does not require any brain atlas.

  14. MRIVIEW: An interactive computational tool for investigation of brain structure and function

    International Nuclear Information System (INIS)

    Ranken, D.; George, J.

    1993-01-01

    MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities

  15. Concordance: Design Ideal for Facilitating Situated Negotiations in Out-of-clinic Healthcare

    DEFF Research Database (Denmark)

    Bagalkot, Naveen L.; Gronvall, Erik; Sokoler, Tomas

    2014-01-01

    Healthcare HCI research has explored various designs that encourage people to follow prescribed treatments, mostly adopting compliance and adherence as design ideals. However, within the medical sciences the notion of concordance also exists. Concordance promotes negotiation between the patient...... and healthcare professional for forging a therapeutic alliance. However, the HCI community has still not adopted concordance as a design ideal. This paper revisits four old design-cases to explore the role of concordance in out-of-clinic healthcare. We argue that concordance, as a design ideal, can guide new...... designs that promote a more active patient-role both at the clinic and beyond....

  16. Geometry Processing of Conventionally Produced Mouse Brain Slice Images.

    Science.gov (United States)

    Agarwal, Nitin; Xu, Xiangmin; Gopi, M

    2018-04-21

    Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as one of the application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. To the best of our knowledge the presented work is the first that automatically registers both clean as well as highly damaged high-resolutions histological slices of mouse brain to a 3D annotated reference atlas space. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Stimulation sites in the subthalamic nucleus projected onto a mean 3-D atlas of the thalamus and basal ganglia.

    Science.gov (United States)

    Sarnthein, Johannes; Péus, Dominik; Baumann-Vogel, Heide; Baumann, Christian R; Sürücü, Oguzkan

    2013-09-01

    In patients with severe forms of Parkinson's disease (PD), deep brain stimulation (DBS) commonly targets the subthalamic nucleus (STN). Recently, the mean 3-D Morel-Atlas of the basal ganglia and the thalamus was introduced. It combines information contained in histological data from ten post-mortem brains. We were interested whether the Morel-Atlas is applicable for the visualization of stimulation sites. In a consecutive PD patient series, we documented preoperative MRI planning, intraoperative target adjustment based on electrophysiological and neurological testing, and perioperative CT target reconstruction. The localization of the DBS electrodes and the optimal stimulation sites were projected onto the Morel-Atlas. We included 20 patients (median age 62 years). The active contact had mean coordinates Xlat = ±12.1 mm, Yap = -1.8 mm, Zvert = -3.2 mm. There was a significant difference between the initially planned site and the coordinates of the postoperative active contact site (median 2.2 mm). The stimulation site was, on average, more anterior and more dorsal. The electrode contact used for optimal stimulation was found within the STN of the atlas in 38/40 (95 %) of implantations. The cluster of stimulation sites in individual patients-as deduced from preoperative MR, intraoperative electrophysiology and neurological testing-showed a high degree of congruence with the atlas. The mean 3D Morel Atlas is thus a useful tool for postoperative target visualization. This represents the first clinical evaluation of the recently created atlas.

  18. Investigating spousal concordance of diabetes through statistical analysis and data mining.

    Directory of Open Access Journals (Sweden)

    Jong-Yi Wang

    Full Text Available Spousal clustering of diabetes merits attention. Whether old-age vulnerability or a shared family environment determines the concordance of diabetes is also uncertain. This study investigated the spousal concordance of diabetes and compared the risk of diabetes concordance between couples and noncouples by using nationally representative data.A total of 22,572 individuals identified from the 2002-2013 National Health Insurance Research Database of Taiwan constituted 5,643 couples and 5,643 noncouples through 1:1 dual propensity score matching (PSM. Factors associated with concordance in both spouses with diabetes were analyzed at the individual level. The risk of diabetes concordance between couples and noncouples was compared at the couple level. Logistic regression was the main statistical method. Statistical data were analyzed using SAS 9.4. C&RT and Apriori of data mining conducted in IBM SPSS Modeler 13 served as a supplement to statistics.High odds of the spousal concordance of diabetes were associated with old age, middle levels of urbanization, and high comorbidities (all P < 0.05. The dual PSM analysis revealed that the risk of diabetes concordance was significantly higher in couples (5.19% than in noncouples (0.09%; OR = 61.743, P < 0.0001.A high concordance rate of diabetes in couples may indicate the influences of assortative mating and shared environment. Diabetes in a spouse implicates its risk in the partner. Family-based diabetes care that emphasizes the screening of couples at risk of diabetes by using the identified risk factors is suggested in prospective clinical practice interventions.

  19. TU-AB-BRA-02: An Efficient Atlas-Based Synthetic CT Generation Method

    International Nuclear Information System (INIS)

    Han, X

    2016-01-01

    Purpose: A major obstacle for MR-only radiotherapy is the need to generate an accurate synthetic CT (sCT) from MR image(s) of a patient for the purposes of dose calculation and DRR generation. We propose here an accurate and efficient atlas-based sCT generation method, which has a computation speed largely independent of the number of atlases used. Methods: Atlas-based sCT generation requires a set of atlases with co-registered CT and MR images. Unlike existing methods that align each atlas to the new patient independently, we first create an average atlas and pre-align every atlas to the average atlas space. When a new patient arrives, we compute only one deformable image registration to align the patient MR image to the average atlas, which indirectly aligns the patient to all pre-aligned atlases. A patch-based non-local weighted fusion is performed in the average atlas space to generate the sCT for the patient, which is then warped back to the original patient space. We further adapt a PatchMatch algorithm that can quickly find top matches between patches of the patient image and all atlas images, which makes the patch fusion step also independent of the number of atlases used. Results: Nineteen brain tumour patients with both CT and T1-weighted MR images are used as testing data and a leave-one-out validation is performed. Each sCT generated is compared against the original CT image of the same patient on a voxel-by-voxel basis. The proposed method produces a mean absolute error (MAE) of 98.6±26.9 HU overall. The accuracy is comparable with a conventional implementation scheme, but the computation time is reduced from over an hour to four minutes. Conclusion: An average atlas space patch fusion approach can produce highly accurate sCT estimations very efficiently. Further validation on dose computation accuracy and using a larger patient cohort is warranted. The author is a full time employee of Elekta, Inc.

  20. 7T MRI subthalamic nucleus atlas for use with 3T MRI.

    Science.gov (United States)

    Milchenko, Mikhail; Norris, Scott A; Poston, Kathleen; Campbell, Meghan C; Ushe, Mwiza; Perlmutter, Joel S; Snyder, Abraham Z

    2018-01-01

    Deep brain stimulation (DBS) of the subthalamic nucleus (STN) reduces motor symptoms in most patients with Parkinson disease (PD), yet may produce untoward effects. Investigation of DBS effects requires accurate localization of the STN, which can be difficult to identify on magnetic resonance images collected with clinically available 3T scanners. The goal of this study is to develop a high-quality STN atlas that can be applied to standard 3T images. We created a high-definition STN atlas derived from seven older participants imaged at 7T. This atlas was nonlinearly registered to a standard template representing 56 patients with PD imaged at 3T. This process required development of methodology for nonlinear multimodal image registration. We demonstrate mm-scale STN localization accuracy by comparison of our 3T atlas with a publicly available 7T atlas. We also demonstrate less agreement with an earlier histological atlas. STN localization error in the 56 patients imaged at 3T was less than 1 mm on average. Our methodology enables accurate STN localization in individuals imaged at 3T. The STN atlas and underlying 3T average template in MNI space are freely available to the research community. The image registration methodology developed in the course of this work may be generally applicable to other datasets.

  1. Receipt of Guideline-Concordant Treatment in Elderly Prostate Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Ronald C., E-mail: Ronald_chen@med.unc.edu [Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Carpenter, William R. [Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Hendrix, Laura H. [Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Bainbridge, John [Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Wang, Andrew Z. [Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Nielsen, Matthew E. [Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); and others

    2014-02-01

    Purpose: To examine the proportion of elderly prostate cancer patients receiving guideline-concordant treatment, using the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database. Methods and Materials: A total of 29,001 men diagnosed in 2004-2007 with localized prostate cancer, aged 66 to 79 years, were included. We characterized the proportion of men who received treatment concordant with the National Comprehensive Cancer Network guidelines, stratified by risk group and age. Logistic regression was used to examine covariates associated with receipt of guideline-concordant management. Results: Guideline concordance was 79%-89% for patients with low- or intermediate-risk disease. Among high-risk patients, 66.6% of those aged 66-69 years received guideline-concordant management, compared with 51.9% of those aged 75-79 years. Discordance was mainly due to conservative management—no treatment or hormone therapy alone. Among the subgroup of patients aged ≤76 years with no measured comorbidity, findings were similar. On multivariable analysis, older age (75-79 vs 66-69 years, odds ratio 0.51, 95% confidence interval 0.50-0.57) was associated with a lower likelihood of guideline concordance for high-risk prostate cancer, but comorbidity was not. Conclusions: There is undertreatment of elderly but healthy patients with high-risk prostate cancer, the most aggressive form of this disease.

  2. Presurgical brain mapping of the language network in patients with brain tumors using resting-state fMRI: Comparison with task fMRI.

    Science.gov (United States)

    Sair, Haris I; Yahyavi-Firouz-Abadi, Noushin; Calhoun, Vince D; Airan, Raag D; Agarwal, Shruti; Intrapiromkul, Jarunee; Choe, Ann S; Gujar, Sachin K; Caffo, Brian; Lindquist, Martin A; Pillai, Jay J

    2016-03-01

    To compare language networks derived from resting-state fMRI (rs-fMRI) with task-fMRI in patients with brain tumors and investigate variables that affect rs-fMRI vs task-fMRI concordance. Independent component analysis (ICA) of rs-fMRI was performed with 20, 30, 40, and 50 target components (ICA20 to ICA50) and language networks identified for patients presenting for presurgical fMRI mapping between 1/1/2009 and 7/1/2015. 49 patients were analyzed fulfilling criteria for presence of brain tumors, no prior brain surgery, and adequate task-fMRI performance. Rs-vs-task-fMRI concordance was measured using Dice coefficients across varying fMRI thresholds before and after noise removal. Multi-thresholded Dice coefficient volume under the surface (DiceVUS) and maximum Dice coefficient (MaxDice) were calculated. One-way Analysis of Variance (ANOVA) was performed to determine significance of DiceVUS and MaxDice between the four ICA order groups. Age, Sex, Handedness, Tumor Side, Tumor Size, WHO Grade, number of scrubbed volumes, image intensity root mean square (iRMS), and mean framewise displacement (FD) were used as predictors for VUS in a linear regression. Artificial elevation of rs-fMRI vs task-fMRI concordance is seen at low thresholds due to noise. Noise-removed group-mean DiceVUS and MaxDice improved as ICA order increased, however ANOVA demonstrated no statistically significant difference between the four groups. Linear regression demonstrated an association between iRMS and DiceVUS for ICA30-50, and iRMS and MaxDice for ICA50. Overall there is moderate group level rs-vs-task fMRI language network concordance, however substantial subject-level variability exists; iRMS may be used to determine reliability of rs-fMRI derived language networks. © 2015 Wiley Periodicals, Inc.

  3. Cyto- and receptor architectonic mapping of the human brain.

    Science.gov (United States)

    Palomero-Gallagher, Nicola; Zilles, Karl

    2018-01-01

    Mapping of the human brain is more than the generation of an atlas-based parcellation of brain regions using histologic or histochemical criteria. It is the attempt to provide a topographically informed model of the structural and functional organization of the brain. To achieve this goal a multimodal atlas of the detailed microscopic and neurochemical structure of the brain must be registered to a stereotaxic reference space or brain, which also serves as reference for topographic assignment of functional data, e.g., functional magnet resonance imaging, electroencephalography, or magnetoencephalography, as well as metabolic imaging, e.g., positron emission tomography. Although classic maps remain pioneering steps, they do not match recent concepts of the functional organization in many regions, and suffer from methodic drawbacks. This chapter provides a summary of the recent status of human brain mapping, which is based on multimodal approaches integrating results of quantitative cyto- and receptor architectonic studies with focus on the cerebral cortex in a widely used reference brain. Descriptions of the methods for observer-independent and statistically testable cytoarchitectonic parcellations, quantitative multireceptor mapping, and registration to the reference brain, including the concept of probability maps and a toolbox for using the maps in functional neuroimaging studies, are provided. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. The role of image registration in brain mapping

    Science.gov (United States)

    Toga, A.W.; Thompson, P.M.

    2008-01-01

    Image registration is a key step in a great variety of biomedical imaging applications. It provides the ability to geometrically align one dataset with another, and is a prerequisite for all imaging applications that compare datasets across subjects, imaging modalities, or across time. Registration algorithms also enable the pooling and comparison of experimental findings across laboratories, the construction of population-based brain atlases, and the creation of systems to detect group patterns in structural and functional imaging data. We review the major types of registration approaches used in brain imaging today. We focus on their conceptual basis, the underlying mathematics, and their strengths and weaknesses in different contexts. We describe the major goals of registration, including data fusion, quantification of change, automated image segmentation and labeling, shape measurement, and pathology detection. We indicate that registration algorithms have great potential when used in conjunction with a digital brain atlas, which acts as a reference system in which brain images can be compared for statistical analysis. The resulting armory of registration approaches is fundamental to medical image analysis, and in a brain mapping context provides a means to elucidate clinical, demographic, or functional trends in the anatomy or physiology of the brain. PMID:19890483

  5. Genotype-Specific Concordance of Chlamydia trachomatis Genital Infection Within Heterosexual Partnerships.

    Science.gov (United States)

    Schillinger, Julia A; Katz, Barry P; Markowitz, Lauri E; Braslins, Phillip G; Shrier, Lydia A; Madico, Guillermo; Van Der Pol, Barbara; Orr, Donald P; Rice, Peter A; Batteiger, Byron E

    2016-12-01

    Sexual transmission rates of Chlamydia trachomatis (Ct) cannot be measured directly; however, the study of concordance of Ct infection in sexual partnerships (dyads) can help to illuminate factors influencing Ct transmission. Heterosexual men and women with Ct infection and their sex partners were enrolled and partner-specific coital and behavioral data collected for the prior 30 days. Microbiological data included Ct culture, and nucleic acid amplification testing (NAAT), quantitative Ct polymerase chain reaction, and ompA genotyping. We measured Ct concordance in dyads and factors (correlates) associated with concordance. One hundred twenty-one women and 125 men formed 128 dyads. Overall, 72.9% of male partners of NAAT-positive women and 68.6% of female partners of NAAT-positive men were Ct-infected. Concordance was more common in dyads with culture-positive members (78.6% of male partners, 77% of female partners). Partners of women and men who were NAAT-positive only had lower concordance (33.3%, 46.4%, respectively). Women in concordant dyads had significantly higher median endocervical quantitative Ct polymerase chain reaction values (3,032) compared with CT-infected women in discordant dyads (1013 inclusion forming units DNA equivalents per mL; P model coitus-specific transmission probabilities.

  6. Gyri of the human parietal lobe: Volumes, spatial extents, automatic labelling, and probabilistic atlases.

    Directory of Open Access Journals (Sweden)

    Heather M Wild

    Full Text Available Accurately describing the anatomy of individual brains enables interlaboratory communication of functional and developmental studies and is crucial for possible surgical interventions. The human parietal lobe participates in multimodal sensory integration including language processing and also contains the primary somatosensory area. We describe detailed protocols to subdivide the parietal lobe, analyze morphological and volumetric characteristics, and create probabilistic atlases in MNI152 stereotaxic space. The parietal lobe was manually delineated on 3D T1 MR images of 30 healthy subjects and divided into four regions: supramarginal gyrus (SMG, angular gyrus (AG, superior parietal lobe (supPL and postcentral gyrus (postCG. There was the expected correlation of male gender with larger brain and intracranial volume. We examined a wide range of anatomical features of the gyri and the sulci separating them. At least a rudimentary primary intermediate sulcus of Jensen (PISJ separating SMG and AG was identified in nearly all (59/60 hemispheres. Presence of additional gyri in SMG and AG was related to sulcal features and volumetric characteristics. The parietal lobe was slightly (2% larger on the left, driven by leftward asymmetries of the postCG and SMG. Intersubject variability was highest for SMG and AG, and lowest for postCG. Overall the morphological characteristics tended to be symmetrical, and volumes also tended to covary between hemispheres. This may reflect developmental as well as maturation factors. To assess the accuracy with which the labels can be used to segment newly acquired (unlabelled T1-weighted brain images, we applied multi-atlas label propagation software (MAPER in a leave-one-out experiment and compared the resulting automatic labels with the manually prepared ones. The results showed strong agreement (mean Jaccard index 0.69, corresponding to a mean Dice index of 0.82, average mean volume error of 0.6%. Stereotaxic

  7. Atlas of neuroanatomy with radiologic correlation and pathologic illustration

    International Nuclear Information System (INIS)

    Dublin, A.B.; Dublin, W.B.

    1982-01-01

    This atlas correlates gross neuroanatomic specimens with radiographs and computed tomographic scans. Pathologic specimens and radiographs are displayed in a similar manner. The first chapter, on embryology, shows the development of the telencephalon, diencephalon, mesencephalon, and metencephalon through a series of overlays. The anatomical section shows the surface of the brain, the ventricles and their adjacent structures, and the vascular system. CT anatomy is demonstrated by correlating CT scans with pathologic brain specimens cut in the axial plane. Pathologic changes associated with congenital malformations, injections, injuries, tumors, and other causes are demonstrated in the last six chapters

  8. Delayed convergence between brain network structure and function in rolandic epilepsy

    Directory of Open Access Journals (Sweden)

    Rene MH Besseling

    2014-09-01

    Full Text Available Introduction Rolandic epilepsy (RE manifests during a critical phase of brain development, and has been associated with language impairments. Concordant abnormalities in structural and functional connectivity (SC and FC have been described before. As SC and FC are under mutual influence, the current study investigates abnormalities in the SC-FC synergy in RE. Methods Twenty-two children with RE (age, mean±SD: 11.3±2.0 y and 22 healthy controls (age 10.5±1.6 y underwent structural, diffusion weighted, and functional MRI at 3T. The probabilistic anatomical landmarks atlas was used to parcellate the (subcortical gray matter. Constrained spherical deconvolution tractography and correlation of time series were used to assess SC and FC, respectively. The SC-FC correlation was assessed as a function of age for the non-zero structural connections over a range of sparsity values (0.01-0.75. A modularity analysis was performed on the mean SC network of the controls to localize potential global effects to subnetworks. SC and FC were also assessed separately using graph analysis.Results The SC-FC correlation was significantly reduced in children with RE compared to healthy controls, especially for the youngest participants. This effect was most pronounced in a left and a right centro-temporal network, as well as in a medial parietal network. Graph analysis revealed no prominent abnormalities in SC or FC network organization.Conclusion Since SC and FC converge during normal maturation, our finding of reduced SC-FC correlation illustrates impaired synergy between brain structure and function. More specifically, since this effect was most pronounced in the youngest participants, RE may represent a developmental disorder of delayed brain network maturation. The observed effects seem especially attributable to medial parietal connections, which forms an intermediate between bilateral centro-temporal modules of epileptiform activity, and bear relevance for

  9. Concordance between Stages of Behavior Change Questionnaire and IPAQ

    Directory of Open Access Journals (Sweden)

    Priscila Missaki Nakamura

    2013-12-01

    Full Text Available A low rate of physical activity (PA participation is observed worldwide. The identification of feasible and reliable instruments able to accurately measuring PA and help in the development of interventions to promote PA are necessary. This study aimed to analyze the concordance between the Stages of Behavior Change Questionnaire (SBCQ and the International Physical Activity Questionnaire (IPAQ long-version in assessing adult leisure-time physical activity (LTPA. A total of 1.588 adults completed the IPAQ to assess LTPA and the participants who performed more than 10 min/week were classified in active individuals. Using the SBCQ, active individuals were those classified in the action or maintenance stage and inactive individuals were those classified in the precontemplation, contemplation or preparation stage. The concordance between SBCQ and IPAQ was found to be 0.80. Separated by gender, it was observed a concordance between the two instruments of 0.82 for women, and 0.77 for men. Regarding age group, it was found to be 0.81 for young and middle-aged adults, and 0.77 for older people. The SBCQ presented a very good concordance with IPAQ to assess LTPA.

  10. The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases

    Directory of Open Access Journals (Sweden)

    Cheng Wei-Cheng

    2006-12-01

    Full Text Available Abstract Background Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. Results We have developed an atlas-viewing application ('NeuARt II' in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years. Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar' either as a standalone or a plug-in application. Conclusion Anatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non

  11. Decision-Making in Pediatric Transport Team Dispatch Using Script Concordance Testing.

    Science.gov (United States)

    Rajapreyar, Prakadeshwari; Marcdante, Karen; Zhang, Liyun; Simpson, Pippa; Meyer, Michael T

    2017-11-01

    Our objective was to compare decision-making in dispatching pediatric transport teams by Medical Directors of pediatric transport teams (serving as experts) to that of Pediatric Intensivists and Critical Care fellows who often serve as Medical Control physicians. Understanding decision-making around team composition and dispatch could impact clinical management, cost effectiveness, and educational needs. Survey was developed using Script Concordance Testing guidelines. The survey contained 15 transport case vignettes covering 20 scenarios (45 questions). Eleven scenarios assessed impact of intrinsic patient factors (e.g., procedural needs), whereas nine assessed extrinsic factors (e.g., weather). Pediatric Critical Care programs accredited by the Accreditation Council for Graduate Medical Education (the United States). Pediatric Intensivists and senior Critical Care fellows at Pediatric Critical Care programs were the target population with Transport Medical Directors serving as the expert panel. None. Survey results were scored per Script Concordance Testing guidelines. Concordance within groups was assessed using simple percentage agreement. There was little concordance in decision-making by Transport Medical Directors (median Script Concordance Testing percentage score [interquartile range] of 33.9 [30.4-37.3]). In addition, there was no statistically significant difference between the median Script Concordance Testing scores among the senior fellows and Pediatric Intensivists (31.1 [29.6-33.2] vs 29.7 [28.3-32.3], respectively; p = 0.12). Transport Medical Directors were more concordant on reasoning involving intrinsic patient factors rather than extrinsic factors (10/21 vs 4/24). Our study demonstrates pediatric transport team dispatch decision-making discordance by pediatric critical care physicians of varying levels of expertise and experience. Script Concordance Testing at a local level may better elucidate standards in medical decision-making within

  12. Three-dimensional interactive atlas of cranial nerve-related disorders.

    Science.gov (United States)

    Nowinski, W L; Chua, B C

    2013-06-01

    Anatomical knowledge of the cranial nerves (CN) is fundamental in education, research and clinical practice. Moreover, understanding CN-related pathology with underlying neuroanatomy and the resulting neurological deficits is of vital importance. To facilitate CN knowledge anatomy and pathology understanding, we created an atlas of CN-related disorders, which is a three-dimensional (3D) interactive tool correlating CN pathology with the underlying surface and sectional neuroanatomy as well as the resulting neurological deficits. A computer platform was developed with: 1) anatomy browser along with the normal brain atlas (built earlier); 2) simulator of CN lesions; 3) tools to label CN-related pathology; and 4) CN pathology database with lesions and disorders, and the resulting signs, symptoms and/or syndromes. The normal neuroanatomy comprises about 2,300 3D components subdivided into modules. Cranial nerves contain more than 600 components: all 12 pairs of cranial nerves (CN I - CN XII) and the brainstem CN nuclei. The CN pathology database was populated with 36 lesions compiled from clinical textbooks. The initial view of each disorder was preset in terms of lesion location and size, surrounding surface and sectional neuroanatomy, and disorder and neuroanatomy labeling. Moreover, path selection from a CN nucleus to a targeted organ further enhances pathology-anatomy relationships. This atlas of CN-related disorders is potentially useful to a wide variety of users ranging from medical students and residents to general practitioners, neuroradiologists and neurologists, as it contains both normal brain anatomy and CN-related pathology correlated with neurological disorders presented in a visual and interactive way.

  13. Advances in ATLAS@Home towards a major ATLAS computing resource

    CERN Document Server

    Cameron, David; The ATLAS collaboration

    2018-01-01

    The volunteer computing project ATLAS@Home has been providing a stable computing resource for the ATLAS experiment since 2013. It has recently undergone some significant developments and as a result has become one of the largest resources contributing to ATLAS computing, by expanding its scope beyond traditional volunteers and into exploitation of idle computing power in ATLAS data centres. Removing the need for virtualization on Linux and instead using container technology has made the entry barrier significantly lower data centre participation and in this paper, we describe the implementation and results of this change. We also present other recent changes and improvements in the project. In early 2017 the ATLAS@Home project was merged into a combined LHC@Home platform, providing a unified gateway to all CERN-related volunteer computing projects. The ATLAS Event Service shifts data processing from file-level to event-level and we describe how ATLAS@Home was incorporated into this new paradigm. The finishing...

  14. High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas

    DEFF Research Database (Denmark)

    Saygin, Z M; Kliemann, D; Iglesias, J. E.

    2017-01-01

    The amygdala is composed of multiple nuclei with unique functions and connections in the limbic system and to the rest of the brain. However, standard in vivo neuroimaging tools to automatically delineate the amygdala into its multiple nuclei are still rare. By scanning postmortem specimens at high...... resolution (100-150µm) at 7T field strength (n = 10), we were able to visualize and label nine amygdala nuclei (anterior amygdaloid, cortico-amygdaloid transition area; basal, lateral, accessory basal, central, cortical medial, paralaminar nuclei). We created an atlas from these labels using a recently...... developed atlas building algorithm based on Bayesian inference. This atlas, which will be released as part of FreeSurfer, can be used to automatically segment nine amygdala nuclei from a standard resolution structural MR image. We applied this atlas to two publicly available datasets (ADNI and ABIDE...

  15. The effect of morphometric atlas selection on multi-atlas-based automatic brachial plexus segmentation

    International Nuclear Information System (INIS)

    Van de Velde, Joris; Wouters, Johan; Vercauteren, Tom; De Gersem, Werner; Achten, Eric; De Neve, Wilfried; Van Hoof, Tom

    2015-01-01

    The present study aimed to measure the effect of a morphometric atlas selection strategy on the accuracy of multi-atlas-based BP autosegmentation using the commercially available software package ADMIRE® and to determine the optimal number of selected atlases to use. Autosegmentation accuracy was measured by comparing all generated automatic BP segmentations with anatomically validated gold standard segmentations that were developed using cadavers. Twelve cadaver computed tomography (CT) atlases were included in the study. One atlas was selected as a patient in ADMIRE®, and multi-atlas-based BP autosegmentation was first performed with a group of morphometrically preselected atlases. In this group, the atlases were selected on the basis of similarity in the shoulder protraction position with the patient. The number of selected atlases used started at two and increased up to eight. Subsequently, a group of randomly chosen, non-selected atlases were taken. In this second group, every possible combination of 2 to 8 random atlases was used for multi-atlas-based BP autosegmentation. For both groups, the average Dice similarity coefficient (DSC), Jaccard index (JI) and Inclusion index (INI) were calculated, measuring the similarity of the generated automatic BP segmentations and the gold standard segmentation. Similarity indices of both groups were compared using an independent sample t-test, and the optimal number of selected atlases was investigated using an equivalence trial. For each number of atlases, average similarity indices of the morphometrically selected atlas group were significantly higher than the random group (p < 0,05). In this study, the highest similarity indices were achieved using multi-atlas autosegmentation with 6 selected atlases (average DSC = 0,598; average JI = 0,434; average INI = 0,733). Morphometric atlas selection on the basis of the protraction position of the patient significantly improves multi-atlas-based BP autosegmentation accuracy

  16. A probabilistic atlas of human brainstem pathways based on connectome imaging data.

    Science.gov (United States)

    Tang, Yuchun; Sun, Wei; Toga, Arthur W; Ringman, John M; Shi, Yonggang

    2018-04-01

    The brainstem is a critical structure that regulates vital autonomic functions, houses the cranial nerves and their nuclei, relays motor and sensory information between the brain and spinal cord, and modulates cognition, mood, and emotions. As a primary relay center, the fiber pathways of the brainstem include efferent and afferent connections among the cerebral cortex, spinal cord, and cerebellum. While diffusion MRI has been successfully applied to map various brain pathways, its application for the in vivo imaging of the brainstem pathways has been limited due to inadequate resolution and large susceptibility-induced distortion artifacts. With the release of high-resolution data from the Human Connectome Project (HCP), there is increasing interest in mapping human brainstem pathways. Previous works relying on HCP data to study brainstem pathways, however, did not consider the prevalence (>80%) of large distortions in the brainstem even after the application of correction procedures from the HCP-Pipeline. They were also limited in the lack of adequate consideration of subject variability in either fiber pathways or region of interests (ROIs) used for bundle reconstruction. To overcome these limitations, we develop in this work a probabilistic atlas of 23 major brainstem bundles using high-quality HCP data passing rigorous quality control. For the large-scale data from the 500-Subject release of HCP, we conducted extensive quality controls to exclude subjects with severe distortions in the brainstem area. After that, we developed a systematic protocol to manually delineate 1300 ROIs on 20 HCP subjects (10 males; 10 females) for the reconstruction of fiber bundles using tractography techniques. Finally, we leveraged our novel connectome modeling techniques including high order fiber orientation distribution (FOD) reconstruction from multi-shell diffusion imaging and topography-preserving tract filtering algorithms to successfully reconstruct the 23 fiber bundles

  17. Contribution of ictal- and interictal brain SPECT to the diagnostic work-up of epileptic patients

    International Nuclear Information System (INIS)

    Dondi, M.; Salgarello, M.; Zoboli, S.; Cidda, C.; Nanni, C.; Rubboli, G.; Meletti, S.; Volpi, L.; Tassinari, C.A.

    2002-01-01

    Aim of the study: We aimed at assessing the contribution of brain SPECT to the diagnostic work-up of patients admitted to the Intensive Epilepsy Monitoring Unit (IEMU) by evaluating concordance of SPECT results with clinical diagnosis (DX) at IEMU admittance (Adm-DX) and at hospital discharge (Disch-DX). Materials and methods: 48 consecutive patients were enrolled in this study and submitted to both ictal and inter-ictal brain SPECT, carried out by means of a three-head system. Before ictal studies, patients were video-EEG monitored in the IEMU. 740 MBq of Tc99m ECD were injected during seizures and imaging performed within 45-60 minutes. For interictal studies, injection was given after at least a 24-hours seizure-free interval. Slices were reconstructed along the orbito-meatal line as well as along the temporal cut. Possible epileptic foci were identified by visual comparison of ictal and interictal studies. Clinical data: Out of the 48 cases, 27 were diagnosed as temporal lobe epilepsies (TLE). Of these, 15 had an Adm-DX of lateralization, whereas 12 were not lateralized according to standardized clinical and EEG criteria. Frontal lobe epilepsy (FLE) was diagnosed in 11 patients, another group of 3 was classified as cryptogenetic (CRYP), while the remaining 7 cases did not fall into any of the previous groups (OTH). SPECT results: in TLE, ictal/interictal SPECT results were congruent with Adm-Dx in 13/27 cases (48%) whereas congruence was found with 25 out of 27 (92%) of Disch-DX. In FLE, concordance between SPECT and clinical diagnosis remained unchanged (9/11 in comparison to either Adm-DX or Disch-DX). CRYPT patients had no lateralization at Adm-DX, while Dis-DX was concordant with SPECT in 2/3 cases. The group labeled as OTH showed concordance SPECT with Adm-DX in 0/7 cases, as opposed to 5/7 of Disch-DX. On the whole, SPECT results were concordant with Adm-DX in 34/48 cases (71%) but concordance was much higher with Dis-DX (41/48; 85%). Conclusions: Brain

  18. ATLAS Outreach Highlights

    CERN Document Server

    Cheatham, Susan; The ATLAS collaboration

    2016-01-01

    The ATLAS outreach team is very active, promoting particle physics to a broad range of audiences including physicists, general public, policy makers, students and teachers, and media. A selection of current outreach activities and new projects will be presented. Recent highlights include the new ATLAS public website and ATLAS Open Data, the very recent public release of 1 fb-1 of ATLAS data.

  19. volBrain: An Online MRI Brain Volumetry System

    Science.gov (United States)

    Manjón, José V.; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

  20. volBrain: an online MRI brain volumetry system

    Directory of Open Access Journals (Sweden)

    Jose V. Manjon

    2016-07-01

    Full Text Available The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es, which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

  1. volBrain: An Online MRI Brain Volumetry System.

    Science.gov (United States)

    Manjón, José V; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

  2. Concordance between European and US case definitions of healthcare-associated infections

    Science.gov (United States)

    2012-01-01

    Background Surveillance of healthcare-associated infections (HAI) is a valuable measure to decrease infection rates. Across Europe, inter-country comparisons of HAI rates seem limited because some countries use US definitions from the US Centers for Disease Control and Prevention (CDC/NHSN) while other countries use European definitions from the Hospitals in Europe Link for Infection Control through Surveillance (HELICS/IPSE) project. In this study, we analyzed the concordance between US and European definitions of HAI. Methods An international working group of experts from seven European countries was set up to identify differences between US and European definitions and then conduct surveillance using both sets of definitions during a three-month period (March 1st -May 31st, 2010). Concordance between case definitions was estimated with Cohen’s kappa statistic (κ). Results Differences in HAI definitions were found for bloodstream infection (BSI), pneumonia (PN), urinary tract infection (UTI) and the two key terms “intensive care unit (ICU)-acquired infection” and “mechanical ventilation”. Concordance was analyzed for these definitions and key terms with the exception of UTI. Surveillance was performed in 47 ICUs and 6,506 patients were assessed. One hundred and eighty PN and 123 BSI cases were identified. When all PN cases were considered, concordance for PN was κ = 0.99 [CI 95%: 0.98-1.00]. When PN cases were divided into subgroups, concordance was κ = 0.90 (CI 95%: 0.86-0.94) for clinically defined PN and κ = 0.72 (CI 95%: 0.63-0.82) for microbiologically defined PN. Concordance for BSI was κ = 0.73 [CI 95%: 0.66-0.80]. However, BSI cases secondary to another infection site (42% of all BSI cases) are excluded when using US definitions and concordance for BSI was κ = 1.00 when only primary BSI cases, i.e. Europe-defined BSI with ”catheter” or “unknown” origin and US-defined laboratory-confirmed BSI (LCBI), were

  3. Concordance between European and US case definitions of healthcare-associated infections

    Directory of Open Access Journals (Sweden)

    Hansen Sonja

    2012-08-01

    Full Text Available Abstract Background Surveillance of healthcare-associated infections (HAI is a valuable measure to decrease infection rates. Across Europe, inter-country comparisons of HAI rates seem limited because some countries use US definitions from the US Centers for Disease Control and Prevention (CDC/NHSN while other countries use European definitions from the Hospitals in Europe Link for Infection Control through Surveillance (HELICS/IPSE project. In this study, we analyzed the concordance between US and European definitions of HAI. Methods An international working group of experts from seven European countries was set up to identify differences between US and European definitions and then conduct surveillance using both sets of definitions during a three-month period (March 1st -May 31st, 2010. Concordance between case definitions was estimated with Cohen’s kappa statistic (κ. Results Differences in HAI definitions were found for bloodstream infection (BSI, pneumonia (PN, urinary tract infection (UTI and the two key terms “intensive care unit (ICU-acquired infection” and “mechanical ventilation”. Concordance was analyzed for these definitions and key terms with the exception of UTI. Surveillance was performed in 47 ICUs and 6,506 patients were assessed. One hundred and eighty PN and 123 BSI cases were identified. When all PN cases were considered, concordance for PN was κ = 0.99 [CI 95%: 0.98-1.00]. When PN cases were divided into subgroups, concordance was κ = 0.90 (CI 95%: 0.86-0.94 for clinically defined PN and κ = 0.72 (CI 95%: 0.63-0.82 for microbiologically defined PN. Concordance for BSI was κ = 0.73 [CI 95%: 0.66-0.80]. However, BSI cases secondary to another infection site (42% of all BSI cases are excluded when using US definitions and concordance for BSI was κ = 1.00 when only primary BSI cases, i.e. Europe-defined BSI with ”catheter” or “unknown” origin and US-defined laboratory-confirmed BSI

  4. Concordance of Beta-papillomavirus across anogenital and oral anatomic sites of men: The HIM Study.

    Science.gov (United States)

    Nunes, Emily M; López, Rossana V M; Sudenga, Staci L; Gheit, Tarik; Tommasino, Massimo; Baggio, Maria L; Ferreira, Silvaneide; Galan, Lenice; Silva, Roberto C; Lazcano-Ponce, Eduardo; Giuliano, Anna R; Villa, Luisa L; Sichero, Laura

    2017-10-01

    We evaluated the concordance between β-HPVs detected in external genital skin, anal canal, and oral cavity specimens collected simultaneously from 717 men that were participating in the multinational HIM Study. Viral genotyping was performed using the Luminex technology. Species- and type-specific concordance was measured using kappa statistics for agreement. Overall, concordance of β-HPVs across sites was low and mainly observed among paired genital/anal canal samples. When grouped by species, solely β-4 HPVs showed moderate concordance in genital/anal pairs (κ = 0.457), which could be attributed to the substantial concordance of HPV-92 in men from Brazil and Mexico (κ > 0.610). β-HPV type concordance was higher in Mexico, where HPV-19 was consistently concordant in all anatomic site combinations. Our analysis indicates that type-specific concordance across sites is limited to few viral types; however, these infections seem to occur more often than would be expected by chance, suggesting that although rare, there is agreement among sites. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. CERN Open Days 2013, Point 1 - ATLAS: ATLAS Experiment

    CERN Multimedia

    CERN Photolab

    2013-01-01

    Stand description: The ATLAS Experiment at CERN is one of the largest and most complex scientific endeavours ever assembled. The detector, located at collision point 1 of the LHC, is designed to explore the fundamental components of nature and to study the forces that shape our universe. The past year’s discovery of a Higgs boson is one of the most important scientific achievements of our time, yet this is only one of many key goals of ATLAS. During a brief break in their journey, some of the 3000-member ATLAS collaboration will be taking time to share the excitement of this exploration with you. On surface no restricted access  The exhibit at Point 1 will give visitors a chance to meet these modern-day explorers and to learn from them how answers to the most fundamental questions of mankind are being sought. Activities will include a visit to the ATLAS detector, located 80m below ground; watching the prize-winning ATLAS movie in the ATLAS cinema; seeing real particle tracks in a cloud chamber and discussi...

  6. Genetic analysis of rare disorders: Bayesian estimation of twin concordance rates

    NARCIS (Netherlands)

    van den Berg, Stéphanie Martine; Hjelmborg, J.

    2012-01-01

    Twin concordance rates provide insight into the possibility of a genetic background for a disease. These concordance rates are usually estimated within a frequentistic framework. Here we take a Bayesian approach. For rare diseases, estimation methods based on asymptotic theory cannot be applied due

  7. The Cognitive Atlas: Towards a knowledge foundation for cognitive neuroscience

    Directory of Open Access Journals (Sweden)

    Russell A Poldrack

    2011-09-01

    Full Text Available Cognitive neuroscience aims to map mental processes onto brain function, which begs the question of what ``mental processes'' exist and how they relate to the tasks that are used to manipulate and measure them. This topic has been addressed informally in prior work, but we propose that cumulative progress in cognitive neuroscience requires a more systematic approach to representing the mental entities that are being mapped to brain function and the tasks used to manipulate and measure mental processes. We describe a new open collaborative project that aims to provide a knowledge base for cognitive neuroscience, called the Cognitive Atlas (accessible online at http://www.cognitiveatlas.org, and outline how this project has the potential to drive novel discoveries about both mind and brain.

  8. Work happiness among teachers: a day reconstruction study on the role of self-concordance.

    Science.gov (United States)

    Tadić, Maja; Bakker, Arnold B; Oerlemans, Wido G M

    2013-12-01

    Self-concordant work motivation arises from one's authentic choices, personal values, and interests. In the present study, we investigated whether self-concordant motivation may fluctuate from one work-related task to the next. On the basis of self-determination theory, we hypothesized that momentary self-concordance buffers the negative impact of momentary work demands on momentary happiness. We developed a modified version of the day reconstruction method to investigate self-concordance, work demands, and happiness during specific work-related tasks on a within-person and within-day level. In total, 132 teachers completed a daily diary on three consecutive work days as well as a background questionnaire. The daily diary resulted in 792 reported work activities and activity-related work demands, self-concordance, and happiness scores. Multilevel analysis showed that-for most work activities-state self-concordant motivation buffered the negative association of work demands with happiness. These findings add to the literature on motivation and well-being by showing that the levels of self-concordance and happiness experienced by employees vary significantly on a within-day level and show a predictable pattern. We discuss theoretical and practical implications of the findings to increase employees' well-being. © 2013.

  9. A three-plane architectonic atlas of the rat hippocampal region.

    Science.gov (United States)

    Boccara, Charlotte N; Kjonigsen, Lisa J; Hammer, Ingvild M; Bjaalie, Jan G; Leergaard, Trygve B; Witter, Menno P

    2015-07-01

    The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource. © 2014 Wiley Periodicals, Inc.

  10. The script concordance test as a tool to evaluate clinical reasoning in neonatology.

    Science.gov (United States)

    Ben Hamida, Emira; Ayadi, Imen; Marrakchi, Zahra; Quinton, André

    2017-05-01

    Script concordance test aims to evaluate knowledge organization, which represents an essential component of the clinical competence. To build a script concordance test and demonstrate its relevance in the evaluation of Neonatology skills. A script concordance test including 20 vignettes and 20 items, was provided to 52 fourth year medical students and 11 family medicine interns. Script concordance test scores obtained by experts were higher then those obtained by students and family medicine interns. The scores (out of 100) were 82.52 ± 7.35 CI95% [77.26-87.78] for the experts, 58.52 ± 9.72 CI95% [55.82-61.23] for the students, and 63.17±11.36 IC95%  [55.53-70.81] (p<0.0001) for the interns. Our data suggest that script concordance tests could be used to assess the acquisition of clinical reasoning among fourth year medical students in neonatolgy.

  11. Voxels in the Brain: Neuroscience, Informatics and Changing Notions of Objectivity.

    Science.gov (United States)

    Beaulieu, Anne

    2001-01-01

    Examines a subset of tools (atlases of the brain) developed in the Human Brain Project (HBP) in order to understand how the use of these tools changes the practice of science. Discusses the redefinition of what constitutes 'objective' neuroscientific knowledge according to both technological possibilities built into these tools and the constraints…

  12. ATLAS Thesis Award 2017

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    Winners of the ATLAS Thesis Award were presented with certificates and glass cubes during a ceremony on 22 February, 2018. They are pictured here with Karl Jakobs (ATLAS Spokesperson), Max Klein (ATLAS Collaboration Board Chair) and Katsuo Tokushuku (ATLAS Collaboration Board Deputy Chair).

  13. ATLAS

    CERN Multimedia

    Akhnazarov, V; Canepa, A; Bremer, J; Burckhart, H; Cattai, A; Voss, R; Hervas, L; Kaplon, J; Nessi, M; Werner, P; Ten kate, H; Tyrvainen, H; Vandelli, W; Krasznahorkay, A; Gray, H; Alvarez gonzalez, B; Eifert, T F; Rolando, G; Oide, H; Barak, L; Glatzer, J; Backhaus, M; Schaefer, D M; Maciejewski, J P; Milic, A; Jin, S; Von torne, E; Limbach, C; Medinnis, M J; Gregor, I; Levonian, S; Schmitt, S; Waananen, A; Monnier, E; Muanza, S G; Pralavorio, P; Talby, M; Tiouchichine, E; Tocut, V M; Rybkin, G; Wang, S; Lacour, D; Laforge, B; Ocariz, J H; Bertoli, W; Malaescu, B; Sbarra, C; Yamamoto, A; Sasaki, O; Koriki, T; Hara, K; Da silva gomes, A; Carvalho maneira, J; Marcalo da palma, A; Chekulaev, S; Tikhomirov, V; Snesarev, A; Buzykaev, A; Maslennikov, A; Peleganchuk, S; Sukharev, A; Kaplan, B E; Swiatlowski, M J; Nef, P D; Schnoor, U; Oakham, G F; Ueno, R; Orr, R S; Abouzeid, O; Haug, S; Peng, H; Kus, V; Vitek, M; Temming, K K; Dang, N P; Meier, K; Schultz-coulon, H; Geisler, M P; Sander, H; Schaefer, U; Ellinghaus, F; Rieke, S; Nussbaumer, A; Liu, Y; Richter, R; Kortner, S; Fernandez-bosman, M; Ullan comes, M; Espinal curull, J; Chiriotti alvarez, S; Caubet serrabou, M; Valladolid gallego, E; Kaci, M; Carrasco vela, N; Lancon, E C; Besson, N E; Gautard, V; Bracinik, J; Bartsch, V C; Potter, C J; Lester, C G; Moeller, V A; Rosten, J; Crooks, D; Mathieson, K; Houston, S C; Wright, M; Jones, T W; Harris, O B; Byatt, T J; Dobson, E; Hodgson, P; Hodgkinson, M C; Dris, M; Karakostas, K; Ntekas, K; Oren, D; Duchovni, E; Etzion, E; Oren, Y; Ferrer, L M; Testa, M; Doria, A; Merola, L; Sekhniaidze, G; Giordano, R; Ricciardi, S; Milazzo, A; Falciano, S; De pedis, D; Dionisi, C; Veneziano, S; Cardarelli, R; Verzegnassi, C; Soualah, R; Ochi, A; Ohshima, T; Kishiki, S; Linde, F L; Vreeswijk, M; Werneke, P; Muijs, A; Vankov, P H; Jansweijer, P P M; Dale, O; Lund, E; Bruckman de renstrom, P; Dabrowski, W; Adamek, J D; Wolters, H; Micu, L; Pantea, D; Tudorache, V; Mjoernmark, J; Klimek, P J; Ferrari, A; Abdinov, O; Akhoundov, A; Hashimov, R; Shelkov, G; Khubua, J; Ladygin, E; Lazarev, A; Glagolev, V; Dedovich, D; Lykasov, G; Zhemchugov, A; Zolnikov, Y; Ryabenko, M; Sivoklokov, S; Vasilyev, I; Shalimov, A; Lobanov, M; Paramoshkina, E; Mosidze, M; Bingul, A; Nodulman, L J; Guarino, V J; Yoshida, R; Drake, G R; Calafiura, P; Haber, C; Quarrie, D R; Alonso, J R; Anderson, C; Evans, H; Lammers, S W; Baubock, M; Anderson, K; Petti, R; Suhr, C A; Linnemann, J T; Richards, R A; Tollefson, K A; Holzbauer, J L; Stoker, D P; Pier, S; Nelson, A J; Isakov, V; Martin, A J; Adelman, J A; Paganini, M; Gutierrez, P; Snow, J M; Pearson, B L; Cleland, W E; Savinov, V; Wong, W; Goodson, J J; Li, H; Lacey, R A; Gordeev, A; Gordon, H; Lanni, F; Nevski, P; Rescia, S; Kierstead, J A; Liu, Z; Yu, W W H; Bensinger, J; Hashemi, K S; Bogavac, D; Cindro, V; Hoeferkamp, M R; Coelli, S; Iodice, M; Piegaia, R N; Alonso, F; Wahlberg, H P; Barberio, E L; Limosani, A; Rodd, N L; Jennens, D T; Hill, E C; Pospisil, S; Smolek, K; Schaile, D A; Rauscher, F G; Adomeit, S; Mattig, P M; Wahlen, H; Volkmer, F; Calvente lopez, S; Sanchis peris, E J; Pallin, D; Podlyski, F; Says, L; Boumediene, D E; Scott, W; Phillips, P W; Greenall, A; Turner, P; Gwilliam, C B; Kluge, T; Wrona, B; Sellers, G J; Millward, G; Adragna, P; Hartin, A; Alpigiani, C; Piccaro, E; Bret cano, M; Hughes jones, R E; Mercer, D; Oh, A; Chavda, V S; Carminati, L; Cavasinni, V; Fedin, O; Patrichev, S; Ryabov, Y; Nesterov, S; Grebenyuk, O; Sasso, J; Mahmood, H; Polsdofer, E; Dai, T; Ferretti, C; Liu, H; Hegazy, K H; Benjamin, D P; Zobernig, G; Ban, J; Brooijmans, G H; Keener, P; Williams, H H; Le geyt, B C; Hines, E J; Fadeyev, V; Schumm, B A; Law, A T; Kuhl, A D; Neubauer, M S; Shang, R; Gagliardi, G; Calabro, D; Conta, C; Zinna, M; Jones, G; Li, J; Stradling, A R; Hadavand, H K; Mcguigan, P; Chiu, P; Baldelomar, E; Stroynowski, R A; Kehoe, R L; De groot, N; Timmermans, C; Lach-heb, F; Addy, T N; Nakano, I; Moreno lopez, D; Grosse-knetter, J; Tyson, B; Rude, G D; Tafirout, R; Benoit, P; Danielsson, H O; Elsing, M; Fassnacht, P; Froidevaux, D; Ganis, G; Gorini, B; Lasseur, C; Lehmann miotto, G; Kollar, D; Aleksa, M; Sfyrla, A; Duehrssen-debling, K; Fressard-batraneanu, S; Van der ster, D C; Bortolin, C; Schumacher, J; Mentink, M; Geich-gimbel, C; Yau wong, K H; Lafaye, R; Crepe-renaudin, S; Albrand, S; Hoffmann, D; Pangaud, P; Meessen, C; Hrivnac, J; Vernay, E; Perus, A; Henrot versille, S L; Le dortz, O; Derue, F; Piccinini, M; Polini, A; Terada, S; Arai, Y; Ikeno, M; Fujii, H; Nagano, K; Ukegawa, F; Aguilar saavedra, J A; Conde muino, P; Castro, N F; Eremin, V; Kopytine, M; Sulin, V; Tsukerman, I; Korol, A; Nemethy, P; Bartoldus, R; Glatte, A; Chelsky, S; Van nieuwkoop, J; Bellerive, A; Sinervo, J K; Battaglia, A; Barbier, G J; Pohl, M; Rosselet, L; Alexandre, G B; Prokoshin, F; Pezoa rivera, R A; Batkova, L; Kladiva, E; Stastny, J; Kubes, T; Vidlakova, Z; Esch, H; Homann, M; Herten, L G; Zimmermann, S U; Pfeifer, B; Stenzel, H; Andrei, G V; Wessels, M; Buescher, V; Kleinknecht, K; Fiedler, F M; Schroeder, C D; Fernandez, E; Mir martinez, L; Vorwerk, V; Bernabeu verdu, J; Salt, J; Civera navarrete, J V; Bernard, R; Berriaud, C P; Chevalier, L P; Hubbard, R; Schune, P; Nikolopoulos, K; Batley, J R; Brochu, F M; Phillips, A W; Teixeira-dias, P J; Rose, M B D; Buttar, C; Buckley, A G; Nurse, E L; Larner, A B; Boddy, C; Henderson, J; Costanzo, D; Tarem, S; Maccarrone, G; Laurelli, P F; Alviggi, M; Chiaramonte, R; Izzo, V; Palumbo, V; Fraternali, M; Crosetti, G; Marchese, F; Yamaguchi, Y; Hessey, N P; Mechnich, J M; Liebig, W; Kastanas, K A; Sjursen, T B; Zalieckas, J; Cameron, D G; Banka, P; Kowalewska, A B; Dwuznik, M; Mindur, B; Boldea, V; Hedberg, V; Smirnova, O; Sellden, B; Allahverdiyev, T; Gornushkin, Y; Koultchitski, I; Tokmenin, V; Chizhov, M; Gongadze, A; Khramov, E; Sadykov, R; Krasnoslobodtsev, I; Smirnova, L; Kramarenko, V; Minaenko, A; Zenin, O; Beddall, A J; Ozcan, E V; Hou, S; Wang, S; Moyse, E; Willocq, S; Chekanov, S; Le compte, T J; Love, J R; Ciocio, A; Hinchliffe, I; Tsulaia, V; Gomez, A; Luehring, F; Zieminska, D; Huth, J E; Gonski, J L; Oreglia, M; Tang, F; Shochet, M J; Costin, T; Mcleod, A; Uzunyan, S; Martin, S P; Pope, B G; Schwienhorst, R H; Brau, J E; Ptacek, E S; Milburn, R H; Sabancilar, E; Lauer, R; Saleem, M; Mohamed meera lebbai, M R; Lou, X; Reeves, K B; Rijssenbeek, M; Novakova, P N; Rahm, D; Steinberg, P A; Wenaus, T J; Paige, F; Ye, S; Kotcher, J R; Assamagan, K A; Oliveira damazio, D; Maeno, T; Henry, A; Dushkin, A; Costa, G; Meroni, C; Resconi, S; Lari, T; Biglietti, M; Lohse, T; Gonzalez silva, M L; Monticelli, F G; Saavedra, A F; Patel, N D; Ciodaro xavier, T; Asevedo nepomuceno, A; Lefebvre, M; Albert, J E; Kubik, P; Faltova, J; Turecek, D; Solc, J; Schaile, O; Ebke, J; Losel, P J; Zeitnitz, C; Sturm, P D; Barreiro alonso, F; Modesto alapont, P; Soret medel, J; Garzon alama, E J; Gee, C N; Mccubbin, N A; Sankey, D; Emeliyanov, D; Dewhurst, A L; Houlden, M A; Klein, M; Burdin, S; Lehan, A K; Eisenhandler, E; Lloyd, S; Traynor, D P; Ibbotson, M; Marshall, R; Pater, J; Freestone, J; Masik, J; Haughton, I; Manousakis katsikakis, A; Sampsonidis, D; Krepouri, A; Roda, C; Sarri, F; Fukunaga, C; Nadtochiy, A; Kara, S O; Timm, S; Alam, S M; Rashid, T; Goldfarb, S; Espahbodi, S; Marley, D E; Rau, A W; Dos anjos, A R; Haque, S; Grau, N C; Havener, L B; Thomson, E J; Newcomer, F M; Hansl-kozanecki, G; Deberg, H A; Takeshita, T; Goggi, V; Ennis, J S; Olness, F I; Kama, S; Ordonez sanz, G; Koetsveld, F; Elamri, M; Mansoor-ul-islam, S; Lemmer, B; Kawamura, G; Bindi, M; Schulte, S; Kugel, A; Kretz, M P; Kurchaninov, L; Blanchot, G; Chromek-burckhart, D; Di girolamo, B; Francis, D; Gianotti, F; Nordberg, M Y; Pernegger, H; Roe, S; Boyd, J; Wilkens, H G; Pauly, T; Fabre, C; Tricoli, A; Bertet, D; Ruiz martinez, M A; Arnaez, O L; Lenzi, B; Boveia, A J; Gillberg, D I; Davies, J M; Zimmermann, R; Uhlenbrock, M; Kraus, J K; Narayan, R T; John, A; Dam, M; Padilla aranda, C; Bellachia, F; Le flour chollet, F M; Jezequel, S; Dumont dayot, N; Fede, E; Mathieu, M; Gensolen, F D; Alio, L; Arnault, C; Bouchel, M; Ducorps, A; Kado, M M; Lounis, A; Zhang, Z P; De vivie de regie, J; Beau, T; Bruni, A; Bruni, G; Grafstrom, P; Romano, M; Lasagni manghi, F; Massa, L; Shaw, K; Ikegami, Y; Tsuno, S; Kawanishi, Y; Benincasa, G; Blagov, M; Fedorchuk, R; Shatalov, P; Romaniouk, A; Belotskiy, K; Timoshenko, S; Hooft van huysduynen, L; Lewis, G H; Wittgen, M M; Mader, W F; Rudolph, C J; Gumpert, C; Mamuzic, J; Rudolph, G; Schmid, P; Corriveau, F; Belanger-champagne, C; Yarkoni, S; Leroy, C; Koffas, T; Harack, B D; Weber, M S; Beck, H; Leger, A; Gonzalez sevilla, S; Zhu, Y; Gao, J; Zhang, X; Blazek, T; Rames, J; Sicho, P; Kouba, T; Sluka, T; Lysak, R; Ristic, B; Kompatscher, A E; Von radziewski, H; Groll, M; Meyer, C P; Oberlack, H; Stonjek, S M; Cortiana, G; Werthenbach, U; Ibragimov, I; Czirr, H S; Cavalli-sforza, M; Puigdengoles olive, C; Tallada crespi, P; Marti i garcia, S; Gonzalez de la hoz, S; Guyot, C; Meyer, J; Schoeffel, L O; Garvey, J; Hawkes, C; Hillier, S J; Staley, R J; Salvatore, P F; Santoyo castillo, I; Carter, J; Yusuff, I B; Barlow, N R; Berry, T S; Savage, G; Wraight, K G; Steele, G E; Hughes, G; Walder, J W; Love, P A; Crone, G J; Waugh, B M; Boeser, S; Sarkar, A M; Holmes, A; Massey, R; Pinder, A; Nicholson, R; Korolkova, E; Katsoufis, I; Maltezos, S; Tsipolitis, G; Leontsinis, S; Levinson, L J; Shoa, M; Abramowicz, H E; Bella, G; Gershon, A; Urkovsky, E; Taiblum, N; Gatti, C; Della pietra, M; Lanza, A; Negri, A; Flaminio, V; Lacava, F; Petrolo, E; Pontecorvo, L; Rosati, S; Zanello, L; Pasqualucci, E; Di ciaccio, A; Giordani, M; Yamazaki, Y; Jinno, T; Nomachi, M; De jong, P J; Ferrari, P; Homma, J; Van der graaf, H; Igonkina, O B; Stugu, B S; Buanes, T; Pedersen, M; Turala, M; Olszewski, A J; Koperny, S Z; Onofre, A; Castro nunes fiolhais, M; Alexa, C; Cuciuc, C M; Akesson, T P A; Hellman, S L; Milstead, D A; Bondyakov, A; Pushnova, V; Budagov, Y; Minashvili, I; Romanov, V; Sniatkov, V; Tskhadadze, E; Kalinovskaya, L; Shalyugin, A; Tavkhelidze, A; Rumyantsev, L; Karpov, S; Soloshenko, A; Vostrikov, A; Borissov, E; Solodkov, A; Vorob'ev, A; Sidorov, S; Malyaev, V; Lee, S; Grudzinski, J J; Virzi, J S; Vahsen, S E; Lys, J; Penwell, J W; Yan, Z; Bernard, C S; Barreiro guimaraes da costa, J P; Oliver, J N; Merritt, F S; Brubaker, E M; Kapliy, A; Kim, J; Zutshi, V V; Burghgrave, B O; Abolins, M A; Arabidze, G; Caughron, S A; Frey, R E; Radloff, P T; Schernau, M; Murillo garcia, R; Porter, R A; Mccormick, C A; Karn, P J; Sliwa, K J; Demers konezny, S M; Strauss, M G; Mueller, J A; Izen, J M; Klimentov, A; Lynn, D; Polychronakos, V; Radeka, V; Sondericker, J I I I; Bathe, S; Duffin, S; Chen, H; De castro faria salgado, P E; Kersevan, B P; Lacker, H M; Schulz, H; Kubota, T; Tan, K G; Yabsley, B D; Nunes de moura junior, N; Pinfold, J; Soluk, R A; Ouellette, E A; Leitner, R; Sykora, T; Solar, M; Sartisohn, G; Hirschbuehl, D; Huning, D; Fischer, J; Terron cuadrado, J; Glasman kuguel, C B; Lacasta llacer, C; Lopez-amengual, J; Calvet, D; Chevaleyre, J; Daudon, F; Montarou, G; Guicheney, C; Calvet, S P J; Tyndel, M; Dervan, P J; Maxfield, S J; Hayward, H S; Beck, G; Cox, B; Da via, C; Paschalias, P; Manolopoulou, M; Ragusa, F; Cimino, D; Ezzi, M; Fiuza de barros, N F; Yildiz, H; Ciftci, A K; Turkoz, S; Zain, S B; Tegenfeldt, F; Chapman, J W; Panikashvili, N; Bocci, A; Altheimer, A D; Martin, F F; Fratina, S; Jackson, B D; Grillo, A A; Seiden, A; Watts, G T; Mangiameli, S; Johns, K A; O'grady, F T; Errede, D R; Darbo, G; Ferretto parodi, A; Leahu, M C; Farbin, A; Ye, J; Liu, T; Wijnen, T A; Naito, D; Takashima, R; Sandoval usme, C E; Zinonos, Z; Moreno llacer, M; Agricola, J B; Mcgovern, S A; Sakurai, Y; Trigger, I M; Qing, D; De silva, A S; Butin, F; Dell'acqua, A; Hawkings, R J; Lamanna, M; Mapelli, L; Passardi, G; Rembser, C; Tremblet, L; Andreazza, W; Dobos, D A; Koblitz, B; Bianco, M; Dimitrov, G V; Schlenker, S; Armbruster, A J; Rammensee, M C; Romao rodrigues, L F; Peters, K; Pozo astigarraga, M E; Yi, Y; Desch, K K; Huegging, F G; Muller, K K; Stillings, J A; Schaetzel, S; Xella, S; Hansen, J D; Colas, J; Daguin, G; Wingerter, I; Ionescu, G D; Ledroit, F; Lucotte, A; Clement, B E; Stark, J; Clemens, J; Djama, F; Knoops, E; Coadou, Y; Vigeolas-choury, E; Feligioni, L; Iconomidou-fayard, L; Imbert, P; Schaffer, A C; Nikolic, I; Trincaz-duvoid, S; Warin, P; Camard, A F; Ridel, M; Pires, S; Giacobbe, B; Spighi, R; Villa, M; Negrini, M; Sato, K; Gavrilenko, I; Akimov, A; Khovanskiy, V; Talyshev, A; Voronkov, A; Hakobyan, H; Mallik, U; Shibata, A; Konoplich, R; Barklow, T L; Koi, T; Straessner, A; Stelzer, B; Robertson, S H; Vachon, B; Stoebe, M; Keyes, R A; Wang, K; Billoud, T R V; Strickland, V; Batygov, M; Krieger, P; Palacino caviedes, G D; Gay, C W; Jiang, Y; Han, L; Liu, M; Zenis, T; Lokajicek, M; Staroba, P; Tasevsky, M; Popule, J; Svatos, M; Seifert, F; Landgraf, U; Lai, S T; Schmitt, K H; Achenbach, R; Schuh, N; Kiesling, C; Macchiolo, A; Nisius, R; Schacht, P; Von der schmitt, J G; Kortner, O; Atlay, N B; Segura sole, E; Grinstein, S; Neissner, C; Bruckner, D M; Oliver garcia, E; Boonekamp, M; Perrin, P; Gaillot, F M; Wilson, J A; Thomas, J P; Thompson, P D; Palmer, J D; Falk, I E; Chavez barajas, C A; Sutton, M R; Robinson, D; Kaneti, S A; Wu, T; Robson, A; Shaw, C; Buzatu, A; Qin, G; Jones, R; Bouhova-thacker, E V; Viehhauser, G; Weidberg, A R; Gilbert, L; Johansson, P D C; Orphanides, M; Vlachos, S; Behar harpaz, S; Papish, O; Lellouch, D J H; Turgeman, D; Benary, O; La rotonda, L; Vena, R; Tarasio, A; Marzano, F; Gabrielli, A; Di stante, L; Liberti, B; Aielli, G; Oda, S; Nozaki, M; Takeda, H; Hayakawa, T; Miyazaki, K; Maeda, J; Sugimoto, T; Pettersson, N E; Bentvelsen, S; Groenstege, H L; Lipniacka, A; Vahabi, M; Ould-saada, F; Chwastowski, J J; Hajduk, Z; Kaczmarska, A; Olszowska, J B; Trzupek, A; Staszewski, R P; Palka, M; Constantinescu, S; Jarlskog, G; Lundberg, B L A; Pearce, M; Ellert, M F; Bannikov, A; Fechtchenko, A; Iambourenko, V; Kukhtin, V; Pozdniakov, V; Topilin, N; Vorozhtsov, S; Khassanov, A; Fliaguine, V; Kharchenko, D; Nikolaev, K; Kotenov, K; Kozhin, A; Zenin, A; Ivashin, A; Golubkov, D; Beddall, A; Su, D; Dallapiccola, C J; Cranshaw, J M; Price, L; Stanek, R W; Gieraltowski, G; Zhang, J; Gilchriese, M; Shapiro, M; Ahlen, S; Morii, M; Taylor, F E; Miller, R J; Phillips, F H; Torrence, E C; Wheeler, S J; Benedict, B H; Napier, A; Hamilton, S F; Petrescu, T A; Boyd, G R J; Jayasinghe, A L; Smith, J M; Mc carthy, R L; Adams, D L; Le vine, M J; Zhao, X; Patwa, A M; Baker, M; Kirsch, L; Krstic, J; Simic, L; Filipcic, A; Seidel, S C; Cantore-cavalli, D; Baroncelli, A; Kind, O M; Scarcella, M J; Maidantchik, C L L; Seixas, J; Balabram filho, L E; Vorobel, V; Spousta, M; Strachota, P; Vokac, P; Slavicek, T; Bergmann, B L; Biebel, O; Kersten, S; Srinivasan, M; Trefzger, T; Vazeille, F; Insa, C; Kirk, J; Middleton, R; Burke, S; Klein, U; Morris, J D; Ellis, K V; Millward, L R; Giokaris, N; Ioannou, P; Angelidakis, S; Bouzakis, K; Andreazza, A; Perini, L; Chtcheguelski, V; Spiridenkov, E; Yilmaz, M; Kaya, U; Ernst, J; Mahmood, A; Saland, J; Kutnink, T; Holler, J; Kagan, H P; Wang, C; Pan, Y; Xu, N; Ji, H; Willis, W J; Tuts, P M; Litke, A; Wilder, M; Rothberg, J; Twomey, M S; Rizatdinova, F; Loch, P; Rutherfoord, J P; Varnes, E W; Barberis, D; Osculati-becchi, B; Brandt, A G; Turvey, A J; Benchekroun, D; Nagasaka, Y; Thanakornworakij, T; Quadt, A; Nadal serrano, J; Magradze, E; Nackenhorst, O; Musheghyan, H; Kareem, M; Chytka, L; Perez codina, E; Stelzer-chilton, O; Brunel, B; Henriques correia, A M; Dittus, F; Hatch, M; Haug, F; Hauschild, M; Huhtinen, M; Lichard, P; Schuh-erhard, S; Spigo, G; Avolio, G; Tsarouchas, C; Ahmad, I; Backes, M P; Barisits, M; Gadatsch, S; Cerv, M; Sicoe, A D; Nattamai sekar, L P; Fazio, D; Shan, L; Sun, X; Gaycken, G F; Hemperek, T; Petersen, T C; Alonso diaz, A; Moynot, M; Werlen, M; Hryn'ova, T; Gallin-martel, M; Wu, M; Touchard, F; Menouni, M; Fougeron, D; Le guirriec, E; Chollet, J C; Veillet, J; Barrillon, P; Prat, S; Krasny, M W; Roos, L; Boudarham, G; Lefebvre, G; Boscherini, D; Valentinetti, S; Acharya, B S; Miglioranzi, S; Kanzaki, J; Unno, Y; Yasu, Y; Iwasaki, H; Tokushuku, K; Maio, A; Rodrigues fernandes, B J; Pinto figueiredo raimundo ribeiro, N M; Bot, A; Shmeleva, A; Zaidan, R; Djilkibaev, R; Mincer, A I; Salnikov, A; Aracena, I A; Schwartzman, A G; Silverstein, D J; Fulsom, B G; Anulli, F; Kuhn, D; White, M J; Vetterli, M J; Stockton, M C; Mantifel, R L; Azuelos, G; Shoaleh saadi, D; Savard, P; Clark, A; Ferrere, D; Gaumer, O P; Diaz gutierrez, M A; Liu, Y; Dubnickova, A; Sykora, I; Strizenec, P; Weichert, J; Zitek, K; Naumann, T; Goessling, C; Klingenberg, R; Jakobs, K; Rurikova, Z; Werner, M W; Arnold, H R; Buscher, D; Hanke, P; Stamen, R; Dietzsch, T A; Kiryunin, A; Salihagic, D; Buchholz, P; Pacheco pages, A; Sushkov, S; Porto fernandez, M D C; Cruz josa, R; Vos, M A; Schwindling, J; Ponsot, P; Charignon, C; Kivernyk, O; Goodrick, M J; Hill, J C; Green, B J; Quarman, C V; Bates, R L; Allwood-spiers, S E; Quilty, D; Chilingarov, A; Long, R E; Barton, A E; Konstantinidis, N; Simmons, B; Davison, A R; Christodoulou, V; Wastie, R L; Gallas, E J; Cox, J; Dehchar, M; Behr, J K; Pickering, M A; Filippas, A; Panagoulias, I; Tenenbaum katan, Y D; Roth, I; Pitt, M; Citron, Z H; Benhammou, Y; Amram, N Y N; Soffer, A; Gorodeisky, R; Antonelli, M; Chiarella, V; Curatolo, M; Esposito, B; Nicoletti, G; Martini, A; Sansoni, A; Carlino, G; Del prete, T; Bini, C; Vari, R; Kuna, M; Pinamonti, M; Itoh, Y; Colijn, A P; Klous, S; Garitaonandia elejabarrieta, H; Rosendahl, P L; Taga, A V; Malecki, P; Malecki, P; Wolter, M W; Kowalski, T; Korcyl, G M; Caprini, M; Caprini, I; Dita, P; Olariu, A; Tudorache, A; Lytken, E; Hidvegi, A; Aliyev, M; Alexeev, G; Bardin, D; Kakurin, S; Lebedev, A; Golubykh, S; Chepurnov, V; Gostkin, M; Kolesnikov, V; Karpova, Z; Davkov, K I; Yeletskikh, I; Grishkevich, Y; Rud, V; Myagkov, A; Nikolaenko, V; Starchenko, E; Zaytsev, A; Fakhrutdinov, R; Cheine, I; Istin, S; Sahin, S; Teng, P; Chu, M L; Trilling, G H; Heinemann, B; Richoz, N; Degeorge, C; Youssef, S; Pilcher, J; Cheng, Y; Purohit, M V; Kravchenko, A; Calkins, R E; Blazey, G; Hauser, R; Koll, J D; Reinsch, A; Brost, E C; Allen, B W; Lankford, A J; Ciobotaru, M D; Slagle, K J; Haffa, B; Mann, A; Loginov, A; Cummings, J T; Loyal, J D; Skubic, P L; Boudreau, J F; Lee, B E; Redlinger, G; Wlodek, T; Carcassi, G; Sexton, K A; Yu, D; Deng, W; Metcalfe, J E; Panitkin, S; Sijacki, D; Mikuz, M; Kramberger, G; Tartarelli, G F; Farilla, A; Stanescu, C; Herrberg, R; Alconada verzini, M J; Brennan, A J; Varvell, K; Marroquim, F; Gomes, A A; Do amaral coutinho, Y; Gingrich, D; Moore, R W; Dolejsi, J; Valkar, S; Broz, J; Jindra, T; Kohout, Z; Kral, V; Mann, A W; Calfayan, P P; Langer, T; Hamacher, K; Sanny, B; Wagner, W; Flick, T; Redelbach, A R; Ke, Y; Higon-rodriguez, E; Donini, J N; Lafarguette, P; Adye, T J; Baines, J; Barnett, B; Wickens, F J; Martin, V J; Jackson, J N; Prichard, P; Kretzschmar, J; Martin, A J; Walker, C J; Potter, K M; Kourkoumelis, C; Tzamarias, S; Houiris, A G; Iliadis, D; Fanti, M; Bertolucci, F; Maleev, V; Sultanov, S; Rosenberg, E I; Krumnack, N E; Bieganek, C; Diehl, E B; Mc kee, S P; Eppig, A P; Harper, D R; Liu, C; Schwarz, T A; Mazor, B; Looper, K A; Wiedenmann, W; Huang, P; Stahlman, J M; Battaglia, M; Nielsen, J A; Zhao, T; Khanov, A; Kaushik, V S; Vichou, E; Liss, A M; Gemme, C; Morettini, P; Parodi, F; Passaggio, S; Rossi, L; Kuzhir, P; Ignatenko, A; Ferrari, R; Spairani, M; Pianori, E; Sekula, S J; Firan, A I; Cao, T; Hetherly, J W; Gouighri, M; Vassilakopoulos, V; Long, M C; Shimojima, M; Sawyer, L H; Brummett, R E; Losada, M A; Schorlemmer, A L; Mantoani, M; Bawa, H S; Mornacchi, G; Nicquevert, B; Palestini, S; Stapnes, S; Veness, R; Kotamaki, M J; Sorde, C; Iengo, P; Campana, S; Goossens, L; Zajacova, Z; Pribyl, L; Poveda torres, J; Marzin, A; Conti, G; Carrillo montoya, G D; Kroseberg, J; Gonella, L; Velz, T; Schmitt, S; Lobodzinska, E M; Lovschall-jensen, A E; Galster, G; Perrot, G; Cailles, M; Berger, N; Barnovska, Z; Delsart, P; Lleres, A; Tisserant, S; Grivaz, J; Matricon, P; Bellagamba, L; Bertin, A; Bruschi, M; De castro, S; Semprini cesari, N; Fabbri, L; Rinaldi, L; Quayle, W B; Truong, T N L; Kondo, T; Haruyama, T; Ng, C; Do valle wemans, A; Almeida veloso, F M; Konovalov, S; Ziegler, J M; Su, D; Lukas, W; Prince, S; Ortega urrego, E J; Teuscher, R J; Knecht, N; Pretzl, K; Borer, C; Gadomski, S; Koch, B; Kuleshov, S; Brooks, W K; Antos, J; Kulkova, I; Chudoba, J; Chyla, J; Tomasek, L; Bazalova, M; Messmer, I; Tobias, J; Sundermann, J E; Kuehn, S S; Kluge, E; Scharf, V L; Barillari, T; Kluth, S; Menke, S; Weigell, P; Schwegler, P; Ziolkowski, M; Casado lechuga, P M; Garcia, C; Sanchez, J; Costa mezquita, M J; Valero biot, J A; Laporte, J; Nikolaidou, R; Virchaux, M; Nguyen, V T H; Charlton, D; Harrison, K; Slater, M W; Newman, P R; Parker, A M; Ward, P; Mcgarvie, S A; Kilvington, G J; D'auria, S; O'shea, V; Mcglone, H M; Fox, H; Henderson, R; Kartvelishvili, V; Davies, B; Sherwood, P; Fraser, J T; Lancaster, M A; Tseng, J C; Hays, C P; Apolle, R; Dixon, S D; Parker, K A; Gazis, E; Papadopoulou, T; Panagiotopoulou, E; Karastathis, N; Hershenhorn, A D; Milov, A; Groth-jensen, J; Bilokon, H; Miscetti, S; Canale, V; Rebuzzi, D M; Capua, M; Bagnaia, P; De salvo, A; Gentile, S; Safai tehrani, F; Solfaroli camillocci, E; Sasao, N; Tsunada, K; Massaro, G; Magrath, C A; Van kesteren, Z; Beker, M G; Van den wollenberg, W; Bugge, L; Buran, T; Read, A L; Gjelsten, B K; Banas, E A; Turnau, J; Derendarz, D K; Kisielewska, D; Chesneanu, D; Rotaru, M; Maurer, J B; Wong, M L; Lund-jensen, B; Asman, B; Jon-and, K B; Silverstein, S B; Johansen, M; Alexandrov, I; Iatsounenko, I; Krumshteyn, Z; Peshekhonov, V; Rybaltchenko, K; Samoylov, V; Cheplakov, A; Kekelidze, G; Lyablin, M; Teterine, V; Bednyakov, V; Kruchonak, U; Shiyakova, M M; Demichev, M; Denisov, S P; Fenyuk, A; Djobava, T; Salukvadze, G; Cetin, S A; Brau, B P; Pais, P R; Proudfoot, J; Van gemmeren, P; Zhang, Q; Beringer, J A; Ely, R; Leggett, C; Pengg, F X; Barnett, M R; Quick, R E; Williams, S; Gardner jr, R W; Huston, J; Brock, R; Wanotayaroj, C; Unel, G N; Taffard, A C; Frate, M; Baker, K O; Tipton, P L; Hutchison, A; Walsh, B J; Norberg, S R; Su, J; Tsybyshev, D; Caballero bejar, J; Ernst, M U; Wellenstein, H; Vudragovic, D; Vidic, I; Gorelov, I V; Toms, K; Alimonti, G; Petrucci, F; Kolanoski, H; Smith, J; Jeng, G; Watson, I J; Guimaraes ferreira, F; Miranda vieira xavier, F; Araujo pereira, R; Poffenberger, P; Sopko, V; Elmsheuser, J; Wittkowski, J; Glitza, K; Gorfine, G W; Ferrer soria, A; Fuster verdu, J A; Sanchis lozano, A; Reinmuth, G; Busato, E; Haywood, S J; Mcmahon, S J; Qian, W; Villani, E G; Laycock, P J; Poll, A J; Rizvi, E S; Foster, J M; Loebinger, F; Forti, A; Plano, W G; Brown, G J A; Kordas, K; Vegni, G; Ohsugi, T; Iwata, Y; Cherkaoui el moursli, R; Sahin, M; Akyazi, E; Carlsen, A; Kanwal, B; Cochran jr, J H; Aronnax, M V; Lockner, M J; Zhou, B; Levin, D S; Weaverdyck, C J; Grom, G F; Rudge, A; Ebenstein, W L; Jia, B; Yamaoka, J; Jared, R C; Wu, S L; Banerjee, S; Lu, Q; Hughes, E W; Alkire, S P; Degenhardt, J D; Lipeles, E D; Spencer, E N; Savine, A; Cheu, E C; Lampl, W; Veatch, J R; Roberts, K; Atkinson, M J; Odino, G A; Polesello, G; Martin, T; White, A P; Stephens, R; Grinbaum sarkisyan, E; Vartapetian, A; Yu, J; Sosebee, M; Thilagar, P A; Spurlock, B; Bonde, R; Filthaut, F; Klok, P; Hoummada, A; Ouchrif, M; Pellegrini, G; Rafi tatjer, J M; Navarro, G A; Blumenschein, U; Weingarten, J C; Mueller, D; Graber, L; Gao, Y; Bode, A; Capeans garrido, M D M; Carli, T; Wells, P; Beltramello, O; Vuillermet, R; Dudarev, A; Salzburger, A; Torchiani, C I; Serfon, C L G; Sloper, J E; Duperrier, G; Lilova, P T; Knecht, M O; Lassnig, M; Anders, G; Deviveiros, P; Young, C; Sforza, F; Shaochen, C; Lu, F; Wermes, N; Wienemann, P; Schwindt, T; Hansen, P H; Hansen, J B; Pingel, A M; Massol, N; Elles, S L; Hallewell, G D; Rozanov, A; Vacavant, L; Fournier, D A; Poggioli, L; Puzo, P M; Tanaka, R; Escalier, M A; Makovec, N; Rezynkina, K; De cecco, S; Cavalleri, P G; Massa, I; Zoccoli, A; Tanaka, S; Odaka, S; Mitsui, S; Tomasio pina, J A; Santos, H F; Satsounkevitch, I; Harkusha, S; Baranov, S; Nechaeva, P; Kayumov, F; Kazanin, V; Asai, M; Mount, R P; Nelson, T K; Smith, D; Kenney, C J; Malone, C M; Kobel, M; Friedrich, F; Grohs, J P; Jais, W J; O'neil, D C; Warburton, A T; Vincter, M; Mccarthy, T G; Groer, L S; Pham, Q T; Taylor, W J; La marra, D; Perrin, E; Wu, X; Bell, W H; Delitzsch, C M; Feng, C; Zhu, C; Tokar, S; Bruncko, D; Kupco, A; Marcisovsky, M; Jakoubek, T; Bruneliere, R; Aktas, A; Narrias villar, D I; Tapprogge, S; Mattmann, J; Kroha, H; Crespo, J; Korolkov, I; Cavallaro, E; Cabrera urban, S; Mitsou, V; Kozanecki, W; Mansoulie, B; Pabot, Y; Etienvre, A; Bauer, F; Chevallier, F; Bouty, A R; Watkins, P; Watson, A; Faulkner, P J W; Curtis, C J; Murillo quijada, J A; Grout, Z J; Chapman, J D; Cowan, G D; George, S; Boisvert, V; Mcmahon, T R; Doyle, A T; Thompson, S A; Britton, D; Smizanska, M; Campanelli, M; Butterworth, J M; Loken, J; Renton, P; Barr, A J; Issever, C; Short, D; Crispin ortuzar, M; Tovey, D R; French, R; Rozen, Y; Alexander, G; Kreisel, A; Conventi, F; Raulo, A; Schioppa, M; Susinno, G; Tassi, E; Giagu, S; Luci, C; Nisati, A; Cobal, M; Ishikawa, A; Jinnouchi, O; Bos, K; Verkerke, W; Vermeulen, J; Van vulpen, I B; Kieft, G; Mora, K D; Olsen, F; Rohne, O M; Pajchel, K; Nilsen, J K; Wosiek, B K; Wozniak, K W; Badescu, E; Jinaru, A; Bohm, C; Johansson, E K; Sjoelin, J B R; Clement, C; Buszello, C P; Huseynova, D; Boyko, I; Popov, B; Poukhov, O; Vinogradov, V; Tsiareshka, P; Skvorodnev, N; Soldatov, A; Chuguev, A; Gushchin, V; Yazici, E; Lutz, M S; Malon, D; Vanyashin, A; Lavrijsen, W; Spieler, H; Biesiada, J L; Bahr, M; Kong, J; Tatarkhanov, M; Ogren, H; Van kooten, R J; Cwetanski, P; Butler, J M; Shank, J T; Chakraborty, D; Ermoline, I; Sinev, N; Whiteson, D O; Corso radu, A; Huang, J; Werth, M P; Kastoryano, M; Meirose da silva costa, B; Namasivayam, H; Hobbs, J D; Schamberger jr, R D; Guo, F; Potekhin, M; Popovic, D; Gorisek, A; Sokhrannyi, G; Hofsajer, I W; Mandelli, L; Ceradini, F; Graziani, E; Giorgi, F; Zur nedden, M E G; Grancagnolo, S; Volpi, M; Nunes hanninger, G; Rados, P K; Milesi, M; Cuthbert, C J; Black, C W; Fink grael, F; Fincke-keeler, M; Keeler, R; Kowalewski, R V; Berghaus, F O; Qi, M; Davidek, T; Tas, P; Jakubek, J; Duckeck, G; Walker, R; Mitterer, C A; Harenberg, T; Sandvoss, S A; Del peso, J; Llorente merino, J; Gonzalez millan, V; Irles quiles, A; Crouau, M; Gris, P L Y; Liauzu, S; Romano saez, S M; Gallop, B J; Jones, T J; Austin, N C; Morris, J; Duerdoth, I; Thompson, R J; Kelly, M P; Leisos, A; Garas, A; Pizio, C; Venda pinto, B A; Kudin, L; Qian, J; Wilson, A W; Mietlicki, D; Long, J D; Sang, Z; Arms, K E; Rahimi, A M; Moss, J J; Oh, S H; Parker, S I; Parsons, J; Cunitz, H; Vanguri, R S; Sadrozinski, H; Lockman, W S; Martinez-mc kinney, G; Goussiou, A; Jones, A; Lie, K; Hasegawa, Y; Olcese, M; Gilewsky, V; Harrison, P F; Janus, M; Spangenberg, M; De, K; Ozturk, N; Pal, A K; Darmora, S; Bullock, D J; Oviawe, O; Derkaoui, J E; Rahal, G; Sircar, A; Frey, A S; Stolte, P; Rosien, N; Zoch, K; Li, L; Schouten, D W; Catinaccio, A; Ciapetti, M; Delruelle, N; Ellis, N; Farthouat, P; Hoecker, A; Klioutchnikova, T; Macina, D; Malyukov, S; Spiwoks, R D; Unal, G P; Vandoni, G; Petersen, B A; Pommes, K; Nairz, A M; Wengler, T; Mladenov, D; Solans sanchez, C A; Lantzsch, K; Schmieden, K; Jakobsen, S; Ritsch, E; Sciuccati, A; Alves dos santos, A M; Ouyang, Q; Zhou, M; Brock, I C; Janssen, J; Katzy, J; Anders, C F; Nilsson, B S; Bazan, A; Di ciaccio, L; Yildizkaya, T; Collot, J; Malek, F; Trocme, B S; Breugnon, P; Godiot, S; Adam bourdarios, C; Coulon, J; Duflot, L; Petroff, P G; Zerwas, D; Lieuvin, M; Calderini, G; Laporte, D; Ocariz, J; Gabrielli, A; Ohska, T K; Kurochkin, Y; Kantserov, V; Vasilyeva, L; Speransky, M; Smirnov, S; Antonov, A; Bulekov, O; Tikhonov, Y; Sargsyan, L; Vardanyan, G; Budick, B; Kocian, M L; Luitz, S; Young, C C; Grenier, P J; Kelsey, M; Black, J E; Kneringer, E; Jussel, P; Horton, A J; Beaudry, J; Chandra, A; Ereditato, A; Topfel, C M; Mathieu, R; Bucci, F; Muenstermann, D; White, R M; He, M; Urban, J; Straka, M; Vrba, V; Schumacher, M; Parzefall, U; Mahboubi, K; Sommer, P O; Koepke, L H; Bethke, S; Moser, H; Wiesmann, M; Walkowiak, W A; Fleck, I J; Martinez-perez, M; Sanchez sanchez, C A; Jorgensen roca, S; Accion garcia, E; Sainz ruiz, C A; Valls ferrer, J A; Amoros vicente, G; Vives torrescasana, R; Ouraou, A; Formica, A; Hassani, S; Watson, M F; Cottin buracchio, G F; Bussey, P J; Saxon, D; Ferrando, J E; Collins-tooth, C L; Hall, D C; Cuhadar donszelmann, T; Dawson, I; Duxfield, R; Argyropoulos, T; Brodet, E; Livneh, R; Shougaev, K; Reinherz, E I; Guttman, N; Beretta, M M; Vilucchi, E; Aloisio, A; Patricelli, S; Caprio, M; Cevenini, F; De vecchi, C; Livan, M; Rimoldi, A; Vercesi, V; Ayad, R; Mastroberardino, A; Ciapetti, G; Luminari, L; Rescigno, M; Santonico, R; Salamon, A; Del papa, C; Kurashige, H; Homma, Y; Tomoto, M; Horii, Y; Sugaya, Y; Hanagaki, K; Bobbink, G; Kluit, P M; Koffeman, E N; Van eijk, B; Lee, H; Eigen, G; Dorholt, O; Strandlie, A; Strzempek, P B; Dita, S; Stoicea, G; Chitan, A; Leven, S S; Moa, T; Brenner, R; Ekelof, T J C; Olshevskiy, A; Roumiantsev, V; Chlachidze, G; Zimine, N; Gusakov, Y; Grigalashvili, N; Mineev, M; Potrap, I; Barashkou, A; Shoukavy, D; Shaykhatdenov, B; Pikelner, A; Gladilin, L; Ammosov, V; Abramov, A; Arik, M; Sahinsoy, M; Uysal, Z; Azizi, K; Hotinli, S C; Zhou, S; Berger, E; Blair, R; Underwood, D G; Einsweiler, K; Garcia-sciveres, M A; Siegrist, J L; Kipnis, I; Dahl, O; Holland, S; Barbaro galtieri, A; Smith, P T; Parua, N; Franklin, M; Mercurio, K M; Tong, B; Pod, E; Cole, S G; Hopkins, W H; Guest, D H; Severini, H; Marsicano, J J; Abbott, B K; Wang, Q; Lissauer, D; Ma, H; Takai, H; Rajagopalan, S; Protopopescu, S D; Snyder, S S; Undrus, A; Popescu, R N; Begel, M A; Blocker, C A; Amelung, C; Mandic, I; Macek, B; Tucker, B H; Citterio, M; Troncon, C; Orestano, D; Taccini, C; Romeo, G L; Dova, M T; Taylor, G N; Gesualdi manhaes, A; Mcpherson, R A; Sobie, R; Taylor, R P; Dolezal, Z; Kodys, P; Slovak, R; Sopko, B; Vacek, V; Sanders, M P; Hertenberger, R; Meineck, C; Becks, K; Kind, P; Sandhoff, M; Cantero garcia, J; De la torre perez, H; Castillo gimenez, V; Ros, E; Hernandez jimenez, Y; Chadelas, R; Santoni, C; Washbrook, A J; O'brien, B J; Wynne, B M; Mehta, A; Vossebeld, J H; Landon, M; Teixeira dias castanheira, M; Cerrito, L; Keates, J R; Fassouliotis, D; Chardalas, M; Manousos, A; Grachev, V; Seliverstov, D; Sedykh, E; Cakir, O; Ciftci, R; Edson, W; Prell, S A; Rosati, M; Stroman, T; Jiang, H; Neal, H A; Li, X; Gan, K K; Smith, D S; Kruse, M C; Ko, B R; Leung fook cheong, A M; Cole, B; Angerami, A R; Greene, Z S; Kroll, J I; Van berg, R P; Forbush, D A; Lubatti, H; Raisher, J; Shupe, M A; Wolin, S; Oshita, H; Gaudio, G; Das, R; Konig, A C; Croft, V A; Harvey, A; Maaroufi, F; Melo, I; Greenwood jr, Z D; Shabalina, E; Mchedlidze, G; Drechsler, E; Rieger, J K; Blackston, M; Colombo, T

    2002-01-01

    % ATLAS \\\\ \\\\ ATLAS is a general-purpose experiment for recording proton-proton collisions at LHC. The ATLAS collaboration consists of 144 participating institutions (June 1998) with more than 1750~physicists and engineers (700 from non-Member States). The detector design has been optimized to cover the largest possible range of LHC physics: searches for Higgs bosons and alternative schemes for the spontaneous symmetry-breaking mechanism; searches for supersymmetric particles, new gauge bosons, leptoquarks, and quark and lepton compositeness indicating extensions to the Standard Model and new physics beyond it; studies of the origin of CP violation via high-precision measurements of CP-violating B-decays; high-precision measurements of the third quark family such as the top-quark mass and decay properties, rare decays of B-hadrons, spectroscopy of rare B-hadrons, and $ B ^0 _{s} $-mixing. \\\\ \\\\The ATLAS dectector, shown in the Figure includes an inner tracking detector inside a 2~T~solenoid providing an axial...

  14. Supporting ATLAS

    CERN Multimedia

    2003-01-01

    Eighteen feet made of stainless steel will support the barrel ATLAS detector in the cavern at Point 1. In total, the ATLAS feet system will carry approximately 6000 tons, and will give the same inclination to the detector as the LHC accelerator. The installation of the feet is scheduled to finish during January 2004 with an installation precision at the 1 mm level despite their height of 5.3 metres. The manufacture was carried out in Russia (Company Izhorskiye Zavody in St. Petersburg), as part of a Russian and JINR Dubna in-kind contribution to ATLAS. Involved in the installation is a team from IHEP-Protvino (Russia), the ATLAS technical co-ordination team at CERN, and the CERN survey team. In all, about 15 people are involved. After the feet are in place, the barrel toroid magnet and the barrel calorimeters will be installed. This will keep the ATLAS team busy for the entire year 2004.

  15. 17 April 2008 - Head of Internal Audit Network meeting visiting the ATLAS experimental area with CERN ATLAS Team Leader P. Fassnacht, ATLAS Technical Coordinator M. Nessi and ATLAS Resources Manager M. Nordberg.

    CERN Multimedia

    Mona Schweizer

    2008-01-01

    17 April 2008 - Head of Internal Audit Network meeting visiting the ATLAS experimental area with CERN ATLAS Team Leader P. Fassnacht, ATLAS Technical Coordinator M. Nessi and ATLAS Resources Manager M. Nordberg.

  16. Delineating Neural Structures of Developmental Human Brains with Diffusion Tensor Imaging

    Directory of Open Access Journals (Sweden)

    Hao Huang

    2010-01-01

    Full Text Available The human brain anatomy is characterized by dramatic structural changes during fetal development. It is extraordinarily complex and yet its origin is a simple tubular structure. Revealing detailed anatomy at different stages of brain development not only aids in understanding this highly ordered process, but also provides clues to detect abnormalities caused by genetic or environmental factors. However, anatomical studies of human brain development during the fetal period are surprisingly scarce and histology-based atlases have become available only recently. Diffusion tensor imaging (DTI measures water diffusion to delineate the underlying neural structures. The high contrasts derived from DTI can be used to establish the brain atlas. With DTI tractography, coherent neural structures, such as white matter tracts, can be three-dimensionally reconstructed. The primary eigenvector of the diffusion tensor can be further explored to characterize microstructures in the cerebral wall of the developmental brains. In this mini-review, the application of DTI in order to reveal the structures of developmental fetal brains has been reviewed in the above-mentioned aspects. The fetal brain DTI provides a unique insight for delineating the neural structures in both macroscopic and microscopic levels. The resultant DTI database will provide structural guidance for the developmental study of human fetal brains in basic neuroscience, and reference standards for diagnostic radiology of premature newborns.

  17. Associating transcription factors and conserved RNA structures with gene regulation in the human brain

    DEFF Research Database (Denmark)

    Hecker, Nikolai; Seemann, Stefan E.; Silahtaroglu, Asli

    2017-01-01

    Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription fac...

  18. Concordance Between Clinical Practice and Published Evidence: Findings From Virginia Commonwealth University School of Dentistry.

    Science.gov (United States)

    Chiang, Harmeet K; Best, Al M; Sarrett, David C

    2017-09-01

    To evaluate the concordance between clinical practice and published evidence by dental faculty and graduating students of the Virginia Commonwealth University School of Dentistry. A questionnaire previously developed by the National Dental Practice-Based Research Network with 12 clinical scenarios was administered to VCU faculty and graduating students. Responses were scored as either consistent or inconsistent with published evidence and then analyzed for differences between dental faculty, graduating students, and the national results. There were 43 dental faculty members with at least half-time student contact who responded to the survey. Faculty concordance ranged from 33% to 100%, and general practice faculty had the highest concordance (82%). Eighty-five of the graduating class of 98 responded to the survey, and student concordance ranged from 18% to 92% and averaged 67%. General practice faculty had higher concordance with published evidence than recently graduated dental students. Graduating students and dental faculty demonstrated higher concordance with evidence-based practice than practitioners in the National Dental Practice-Based Research Network. General practice dental faculty demonstrated adequate concordance, but students demonstrated only a medium-level concordance. Practitioners involved in teaching dental students are better able to keep up with evolving evidence and are better able to demonstrate evidence-based practice. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. White matter atlas of the human spinal cord with estimation of partial volume effect.

    Science.gov (United States)

    Lévy, S; Benhamou, M; Naaman, C; Rainville, P; Callot, V; Cohen-Adad, J

    2015-10-01

    Template-based analysis has proven to be an efficient, objective and reproducible way of extracting relevant information from multi-parametric MRI data. Using common atlases, it is possible to quantify MRI metrics within specific regions without the need for manual segmentation. This method is therefore free from user-bias and amenable to group studies. While template-based analysis is common procedure for the brain, there is currently no atlas of the white matter (WM) spinal pathways. The goals of this study were: (i) to create an atlas of the white matter tracts compatible with the MNI-Poly-AMU template and (ii) to propose methods to quantify metrics within the atlas that account for partial volume effect. The WM atlas was generated by: (i) digitalizing an existing WM atlas from a well-known source (Gray's Anatomy), (ii) registering this atlas to the MNI-Poly-AMU template at the corresponding slice (C4 vertebral level), (iii) propagating the atlas throughout all slices of the template (C1 to T6) using regularized diffeomorphic transformations and (iv) computing partial volume values for each voxel and each tract. Several approaches were implemented and validated to quantify metrics within the atlas, including weighted-average and Gaussian mixture models. Proof-of-concept application was done in five subjects for quantifying magnetization transfer ratio (MTR) in each tract of the atlas. The resulting WM atlas showed consistent topological organization and smooth transitions along the rostro-caudal axis. The median MTR across tracts was 26.2. Significant differences were detected across tracts, vertebral levels and subjects, but not across laterality (right-left). Among the different tested approaches to extract metrics, the maximum a posteriori showed highest performance with respect to noise, inter-tract variability, tract size and partial volume effect. This new WM atlas of the human spinal cord overcomes the biases associated with manual delineation and partial

  20. Sociodemographic Correlates of HIV Discordant and Concordant ...

    African Journals Online (AJOL)

    AIDS is significant. An understanding of the characteristics of HIV- affected couples will help modify preventive strategies. The aim of this study was to compare the HIV discordant and concordant partnerships for sociodemographic ...

  1. Transitions from hospital to community care: the role of patient-provider language concordance.

    Science.gov (United States)

    Rayan, Nosaiba; Admi, Hanna; Shadmi, Efrat

    2014-01-01

    Cultural and language discordance between patients and providers constitutes a significant challenge to provision of quality healthcare. This study aims to evaluate minority patients' discharge from hospital to community care, specifically examining the relationship between patient-provider language concordance and the quality of transitional care. This was a multi-method prospective study of care transitions of 92 patients: native Hebrew, Russian or Arabic speakers, with a pre-discharge questionnaire and structured observations examining discharge preparation from a large Israeli teaching hospital. Two weeks post-discharge patients were surveyed by phone, on the transition from hospital to community care (the Care Transition Measure (CTM-15, 0-100 scale)) and on the primary-care post-discharge visit. Overall, ratings on the CTM indicated fair quality of the transition process (scores of 51.8 to 58.8). Patient-provider language concordance was present in 49% of minority patients' discharge briefings. Language concordance was associated with higher CTM scores among minority groups (64.1 in language-concordant versus 49.8 in non-language-concordant discharges, P Language-concordant care, coupled with extensive discharge briefings and post-discharge explanations for ongoing care, are important contributors to the quality of care transitions of ethnic minority patients.

  2. Concordance measures and second order stochastic dominance-portfolio efficiency analysis

    Czech Academy of Sciences Publication Activity Database

    Kopa, Miloš; Tichý, T.

    2012-01-01

    Roč. 15, č. 4 (2012), s. 110-120 ISSN 1212-3609 R&D Projects: GA ČR(CZ) GBP402/12/G097 Institutional support: RVO:67985556 Keywords : dependency * concordance * portfolio selection * second order stochastic dominance Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.633, year: 2012 http://library.utia.cas.cz/separaty/2013/E/kopa-concordance measures and second order stochastic dominance- portfolio efficiency analysis.pdf

  3. Potential predictors for the amount of intra-operative brain shift during deep brain stimulation surgery

    Science.gov (United States)

    Datteri, Ryan; Pallavaram, Srivatsan; Konrad, Peter E.; Neimat, Joseph S.; D'Haese, Pierre-François; Dawant, Benoit M.

    2011-03-01

    A number of groups have reported on the occurrence of intra-operative brain shift during deep brain stimulation (DBS) surgery. This has a number of implications for the procedure including an increased chance of intra-cranial bleeding and complications due to the need for more exploratory electrodes to account for the brain shift. It has been reported that the amount of pneumocephalus or air invasion into the cranial cavity due to the opening of the dura correlates with intraoperative brain shift. Therefore, pre-operatively predicting the amount of pneumocephalus expected during surgery is of interest toward accounting for brain shift. In this study, we used 64 DBS patients who received bilateral electrode implantations and had a post-operative CT scan acquired immediately after surgery (CT-PI). For each patient, the volumes of the pneumocephalus, left ventricle, right ventricle, third ventricle, white matter, grey matter, and cerebral spinal fluid were calculated. The pneumocephalus was calculated from the CT-PI utilizing a region growing technique that was initialized with an atlas-based image registration method. A multi-atlas-based image segmentation method was used to segment out the ventricles of each patient. The Statistical Parametric Mapping (SPM) software package was utilized to calculate the volumes of the cerebral spinal fluid (CSF), white matter and grey matter. The volume of individual structures had a moderate correlation with pneumocephalus. Utilizing a multi-linear regression between the volume of the pneumocephalus and the statistically relevant individual structures a Pearson's coefficient of r = 0.4123 (p = 0.0103) was found. This study shows preliminary results that could be used to develop a method to predict the amount of pneumocephalus ahead of the surgery.

  4. Probabilistic liver atlas construction.

    Science.gov (United States)

    Dura, Esther; Domingo, Juan; Ayala, Guillermo; Marti-Bonmati, Luis; Goceri, E

    2017-01-13

    Anatomical atlases are 3D volumes or shapes representing an organ or structure of the human body. They contain either the prototypical shape of the object of interest together with other shapes representing its statistical variations (statistical atlas) or a probability map of belonging to the object (probabilistic atlas). Probabilistic atlases are mostly built with simple estimations only involving the data at each spatial location. A new method for probabilistic atlas construction that uses a generalized linear model is proposed. This method aims to improve the estimation of the probability to be covered by the liver. Furthermore, all methods to build an atlas involve previous coregistration of the sample of shapes available. The influence of the geometrical transformation adopted for registration in the quality of the final atlas has not been sufficiently investigated. The ability of an atlas to adapt to a new case is one of the most important quality criteria that should be taken into account. The presented experiments show that some methods for atlas construction are severely affected by the previous coregistration step. We show the good performance of the new approach. Furthermore, results suggest that extremely flexible registration methods are not always beneficial, since they can reduce the variability of the atlas and hence its ability to give sensible values of probability when used as an aid in segmentation of new cases.

  5. Report to users of ATLAS

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1995-05-01

    This report contains discussing in the following areas: Status of the Atlas accelerator; highlights of recent research at Atlas; concept for an advanced exotic beam facility based on Atlas; program advisory committee; Atlas executive committee; and Atlas and ANL physics division on the world wide web

  6. ATLAS Distributed Computing Automation

    CERN Document Server

    Schovancova, J; The ATLAS collaboration; Borrego, C; Campana, S; Di Girolamo, A; Elmsheuser, J; Hejbal, J; Kouba, T; Legger, F; Magradze, E; Medrano Llamas, R; Negri, G; Rinaldi, L; Sciacca, G; Serfon, C; Van Der Ster, D C

    2012-01-01

    The ATLAS Experiment benefits from computing resources distributed worldwide at more than 100 WLCG sites. The ATLAS Grid sites provide over 100k CPU job slots, over 100 PB of storage space on disk or tape. Monitoring of status of such a complex infrastructure is essential. The ATLAS Grid infrastructure is monitored 24/7 by two teams of shifters distributed world-wide, by the ATLAS Distributed Computing experts, and by site administrators. In this paper we summarize automation efforts performed within the ATLAS Distributed Computing team in order to reduce manpower costs and improve the reliability of the system. Different aspects of the automation process are described: from the ATLAS Grid site topology provided by the ATLAS Grid Information System, via automatic site testing by the HammerCloud, to automatic exclusion from production or analysis activities.

  7. [Inter-rater concordance of the "Nursing Activities Score" in intensive care].

    Science.gov (United States)

    Valls-Matarín, Josefa; Salamero-Amorós, Maria; Roldán-Gil, Carmen; Quintana-Riera, Salvador

    2015-01-01

    To evaluate inter-rater concordance in the valuation of the "Nursing Activities Score". Cross-sectional descriptive study conducted from December 2012 until June 2013 in a general intensive care unit with twelve beds. Three evaluator nurses, simultaneously and independently, through the patient daily charts, scored the nursing workload using Nursing Activities Score scale in all patients admitted over 18 years old. Three hundreds and thirty-nine records were collected. The intra-class correlation coefficient (ICC) between evaluators was 0.92 (0.89-0.94). A perfect concordance was obtained in 39.1% of the items, with 52.2% having a high, and 8.7% having lower concordance, corresponding to two of the items with multiple scoring options. Significant differences between two of the evaluators (P=.049) were found. Although the inter-rater concordance was high, more accurate records are needed to reduce the variability of the items with multiple options and to allow more accuracy in the interpretation and measurement of the data regarding nursing workload. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  8. Delayed convergence between brain network structure and function in rolandic epilepsy

    NARCIS (Netherlands)

    Besseling, R.M.H.; Jansen, J.F.A.; Overvliet, G.M.; van der Kruijs, S.J.M.; Ebus, S.C.M.; de Louw, A.J.A.; Hofman, P.A.M.; Aldenkamp, A.P.; Backes, W.H.

    2014-01-01

    INTRODUCTION: Rolandic epilepsy (RE) manifests during a critical phase of brain development, and has been associated with language impairments. Concordant abnormalities in structural and functional connectivity (SC and FC) have been described before. As SC and FC are under mutual influence, the

  9. Estimating the concordance probability in a survival analysis with a discrete number of risk groups.

    Science.gov (United States)

    Heller, Glenn; Mo, Qianxing

    2016-04-01

    A clinical risk classification system is an important component of a treatment decision algorithm. A measure used to assess the strength of a risk classification system is discrimination, and when the outcome is survival time, the most commonly applied global measure of discrimination is the concordance probability. The concordance probability represents the pairwise probability of lower patient risk given longer survival time. The c-index and the concordance probability estimate have been used to estimate the concordance probability when patient-specific risk scores are continuous. In the current paper, the concordance probability estimate and an inverse probability censoring weighted c-index are modified to account for discrete risk scores. Simulations are generated to assess the finite sample properties of the concordance probability estimate and the weighted c-index. An application of these measures of discriminatory power to a metastatic prostate cancer risk classification system is examined.

  10. ATLAS-AWS

    International Nuclear Information System (INIS)

    Gehrcke, Jan-Philip; Stonjek, Stefan; Kluth, Stefan

    2010-01-01

    We show how the ATLAS offline software is ported on the Amazon Elastic Compute Cloud (EC2). We prepare an Amazon Machine Image (AMI) on the basis of the standard ATLAS platform Scientific Linux 4 (SL4). Then an instance of the SLC4 AMI is started on EC2 and we install and validate a recent release of the ATLAS offline software distribution kit. The installed software is archived as an image on the Amazon Simple Storage Service (S3) and can be quickly retrieved and connected to new SL4 AMI instances using the Amazon Elastic Block Store (EBS). ATLAS jobs can then configure against the release kit using the ATLAS configuration management tool (cmt) in the standard way. The output of jobs is exported to S3 before the SL4 AMI is terminated. Job status information is transferred to the Amazon SimpleDB service. The whole process of launching instances of our AMI, starting, monitoring and stopping jobs and retrieving job output from S3 is controlled from a client machine using python scripts implementing the Amazon EC2/S3 API via the boto library working together with small scripts embedded in the SL4 AMI. We report our experience with setting up and operating the system using standard ATLAS job transforms.

  11. EnviroAtlas

    Data.gov (United States)

    City and County of Durham, North Carolina — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  12. On the calculation of brain area shifts due to cerebral tumors

    International Nuclear Information System (INIS)

    Labudde, D.; Hartmann, S.; Synowitz, M.

    2002-01-01

    A precise knowledge of the localization of an intracerebral mass is a basic requirement for the planning of neurosurgical operations. Stereotactic atlases offer the possibility to adapt pre-operative imaging data onto normal anatomical conditions in the CNS. These atlases, however, reflect the standard variants of the CNS and do not allow to draw conclusions on local and secondary changes of the anatomy caused by the presence of pathological processes. The physical model proposed in this paper provides an estimate of the displacement of brain areas by an intracerebral mass. The modeling of brain parenchyma deformation is based on the mechanics of deformed media. The implementation of the model is successful in the group of primary brain tumors and meningiomas, and uses empirically-obtained data of a prospectively-selected patient population. The aim of the proposed model is, as further step, the integration and adaptation in apposite software solutions for the stereotactic orientation in the CNS. (orig.) [de

  13. Dear ATLAS colleagues,

    CERN Multimedia

    PH Department

    2008-01-01

    We are collecting old pairs of glasses to take out to Mali, where they can be re-used by people there. The price for a pair of glasses can often exceed 3 months salary, so they are prohibitively expensive for many people. If you have any old spectacles you can donate, please put them in the special box in the ATLAS secretariat, bldg.40-4-D01 before the Christmas closure on 19 December so we can take them with us when we leave for Africa at the end of the month. (more details in ATLAS e-news edition of 29 September 2008: http://atlas-service-enews.web.cern.ch/atlas-service-enews/news/news_mali.php) many thanks! Katharine Leney co-driver of the ATLAS car on the Charity Run to Mali

  14. Encoding atlases by randomized classification forests for efficient multi-atlas label propagation.

    Science.gov (United States)

    Zikic, D; Glocker, B; Criminisi, A

    2014-12-01

    We propose a method for multi-atlas label propagation (MALP) based on encoding the individual atlases by randomized classification forests. Most current approaches perform a non-linear registration between all atlases and the target image, followed by a sophisticated fusion scheme. While these approaches can achieve high accuracy, in general they do so at high computational cost. This might negatively affect the scalability to large databases and experimentation. To tackle this issue, we propose to use a small and deep classification forest to encode each atlas individually in reference to an aligned probabilistic atlas, resulting in an Atlas Forest (AF). Our classifier-based encoding differs from current MALP approaches, which represent each point in the atlas either directly as a single image/label value pair, or by a set of corresponding patches. At test time, each AF produces one probabilistic label estimate, and their fusion is done by averaging. Our scheme performs only one registration per target image, achieves good results with a simple fusion scheme, and allows for efficient experimentation. In contrast to standard forest schemes, in which each tree would be trained on all atlases, our approach retains the advantages of the standard MALP framework. The target-specific selection of atlases remains possible, and incorporation of new scans is straightforward without retraining. The evaluation on four different databases shows accuracy within the range of the state of the art at a significantly lower running time. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Recent ATLAS Articles on WLAP

    CERN Multimedia

    Goldfarb, S

    2005-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: Atlas Software Week Plenary 6-10 December 2004 North American ATLAS Physics Workshop (Tucson) 20-21 December 2004 (17 talks) Physics Analysis Tools Tutorial (Tucson) 19 December 2004 Full Chain Tutorial 21 September 2004 ATLAS Plenary Sessions, 17-18 February 2005 (17 talks) Coming soon: ATLAS Tutorial on Electroweak Physics, 14 Feb. 2005 Software Workshop, 21-22 February 2005 Click here to browse WLAP for all ATLAS lectures.

  16. Multi-atlas pancreas segmentation: Atlas selection based on vessel structure.

    Science.gov (United States)

    Karasawa, Ken'ichi; Oda, Masahiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Chu, Chengwen; Zheng, Guoyan; Rueckert, Daniel; Mori, Kensaku

    2017-07-01

    Automated organ segmentation from medical images is an indispensable component for clinical applications such as computer-aided diagnosis (CAD) and computer-assisted surgery (CAS). We utilize a multi-atlas segmentation scheme, which has recently been used in different approaches in the literature to achieve more accurate and robust segmentation of anatomical structures in computed tomography (CT) volume data. Among abdominal organs, the pancreas has large inter-patient variability in its position, size and shape. Moreover, the CT intensity of the pancreas closely resembles adjacent tissues, rendering its segmentation a challenging task. Due to this, conventional intensity-based atlas selection for pancreas segmentation often fails to select atlases that are similar in pancreas position and shape to those of the unlabeled target volume. In this paper, we propose a new atlas selection strategy based on vessel structure around the pancreatic tissue and demonstrate its application to a multi-atlas pancreas segmentation. Our method utilizes vessel structure around the pancreas to select atlases with high pancreatic resemblance to the unlabeled volume. Also, we investigate two types of applications of the vessel structure information to the atlas selection. Our segmentations were evaluated on 150 abdominal contrast-enhanced CT volumes. The experimental results showed that our approach can segment the pancreas with an average Jaccard index of 66.3% and an average Dice overlap coefficient of 78.5%. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. ATLAS people can run!

    CERN Multimedia

    Claudia Marcelloni de Oliveira; Pauline Gagnon

    It must be all the training we are getting every day, running around trying to get everything ready for the start of the LHC next year. This year, the ATLAS runners were in fine form and came in force. Nine ATLAS teams signed up for the 37th Annual CERN Relay Race with six runners per team. Under a blasting sun on Wednesday 23rd May 2007, each team covered the distances of 1000m, 800m, 800m, 500m, 500m and 300m taking the runners around the whole Meyrin site, hills included. A small reception took place in the ATLAS secretariat a week later to award the ATLAS Cup to the best ATLAS team. For the details on this complex calculation which takes into account the age of each runner, their gender and the color of their shoes, see the July 2006 issue of ATLAS e-news. The ATLAS Running Athena Team, the only all-women team enrolled this year, won the much coveted ATLAS Cup for the second year in a row. In fact, they are so good that Peter Schmid and Patrick Fassnacht are wondering about reducing the women's bonus in...

  18. Anterior temporal lobe white matter abnormal signal (ATLAS) as an indicator of seizure focus laterality in temporal lobe epilepsy: comparison of double inversion recovery, FLAIR and T2W MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Morimoto, Emiko; Kanagaki, Mitsunori; Okada, Tomohisa; Yamamoto, Akira; Togashi, Kaori [Kyoto University Graduate School of Medicine, Department of Diagnostic Imaging and Nuclear Medicine, Kyoto (Japan); Mori, Nobuyuki [Tenri Hospital, Department of Radiology, Tenri, Nara (Japan); Matsumoto, Riki; Ikeda, Akio; Takahashi, Ryosuke [Kyoto University Graduate School of Medicine, Department of Neurology, Kyoto (Japan); Mikuni, Nobuhiro [Sapporo Medical University, Department of Neurosurgery, Sapporo, Hokkaido (Japan); Kunieda, Takeharu; Miyamoto, Susumu [Kyoto University Graduate School of Medicine, Department of Neurosurgery, Kyoto (Japan); Paul, Dominik [Siemens AG Healthcare Sector, Erlangen (Germany)

    2013-01-15

    To investigate the diagnostic capability of anterior temporal lobe white matter abnormal signal (ATLAS) for determining seizure focus laterality in temporal lobe epilepsy (TLE) by comparing different MR sequences. This prospective study was approved by the institutional review board and written informed consent was obtained. Three 3D sequences (double inversion recovery (DIR), fluid-attenuated inversion recovery (FLAIR) and T2-weighted imaging (T2WI)) and two 2D sequences (FLAIR and T2WI) were acquired at 3 T. Signal changes in the anterior temporal white matter of 21 normal volunteers were evaluated. ATLAS laterality was evaluated in 21 TLE patients. Agreement of independent evaluations by two neuroradiologists was assessed using {kappa} statistics. Differences in concordance between ATLAS laterality and clinically defined seizure focus laterality were analysed using McNemar's test with multiple comparisons. Pre-amygdala high signals (PAHS) were detected in all volunteers only on 3D-DIR. Inter-evaluator agreement was moderate to almost perfect for each sequence. Correct diagnosis of seizure laterality was significantly more frequent on 3D-DIR than on any other sequences (P {<=} 0.031 for each evaluator). The most sensitive sequence for detecting ATLAS laterality was 3D-DIR. ATLAS laterality on 3D-DIR can be a good indicator for determining seizure focus localization in TLE. (orig.)

  19. Anterior temporal lobe white matter abnormal signal (ATLAS) as an indicator of seizure focus laterality in temporal lobe epilepsy: comparison of double inversion recovery, FLAIR and T2W MR imaging

    International Nuclear Information System (INIS)

    Morimoto, Emiko; Kanagaki, Mitsunori; Okada, Tomohisa; Yamamoto, Akira; Togashi, Kaori; Mori, Nobuyuki; Matsumoto, Riki; Ikeda, Akio; Takahashi, Ryosuke; Mikuni, Nobuhiro; Kunieda, Takeharu; Miyamoto, Susumu; Paul, Dominik

    2013-01-01

    To investigate the diagnostic capability of anterior temporal lobe white matter abnormal signal (ATLAS) for determining seizure focus laterality in temporal lobe epilepsy (TLE) by comparing different MR sequences. This prospective study was approved by the institutional review board and written informed consent was obtained. Three 3D sequences (double inversion recovery (DIR), fluid-attenuated inversion recovery (FLAIR) and T2-weighted imaging (T2WI)) and two 2D sequences (FLAIR and T2WI) were acquired at 3 T. Signal changes in the anterior temporal white matter of 21 normal volunteers were evaluated. ATLAS laterality was evaluated in 21 TLE patients. Agreement of independent evaluations by two neuroradiologists was assessed using κ statistics. Differences in concordance between ATLAS laterality and clinically defined seizure focus laterality were analysed using McNemar's test with multiple comparisons. Pre-amygdala high signals (PAHS) were detected in all volunteers only on 3D-DIR. Inter-evaluator agreement was moderate to almost perfect for each sequence. Correct diagnosis of seizure laterality was significantly more frequent on 3D-DIR than on any other sequences (P ≤ 0.031 for each evaluator). The most sensitive sequence for detecting ATLAS laterality was 3D-DIR. ATLAS laterality on 3D-DIR can be a good indicator for determining seizure focus localization in TLE. (orig.)

  20. Recent ATLAS Articles on WLAP

    CERN Multimedia

    J. Herr

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: Atlas Physics Workshop 6-11 June 2005 June 2005 ATLAS Week Plenary Session Click here to browse WLAP for all ATLAS lectures.

  1. DigiWarp: a method for deformable mouse atlas warping to surface topographic data

    International Nuclear Information System (INIS)

    Joshi, Anand A; Shattuck, David W; Toga, Arthur W; Chaudhari, Abhijit J; Li Changqing; Cherry, Simon R; Dutta, Joyita; Leahy, Richard M

    2010-01-01

    For pre-clinical bioluminescence or fluorescence optical tomography, the animal's surface topography and internal anatomy need to be estimated for improving the quantitative accuracy of reconstructed images. The animal's surface profile can be measured by all-optical systems, but estimation of the internal anatomy using optical techniques is non-trivial. A 3D anatomical mouse atlas may be warped to the estimated surface. However, fitting an atlas to surface topography data is challenging because of variations in the posture and morphology of imaged mice. In addition, acquisition of partial data (for example, from limited views or with limited sampling) can make the warping problem ill-conditioned. Here, we present a method for fitting a deformable mouse atlas to surface topographic range data acquired by an optical system. As an initialization procedure, we match the posture of the atlas to the posture of the mouse being imaged using landmark constraints. The asymmetric L 2 pseudo-distance between the atlas surface and the mouse surface is then minimized in order to register two data sets. A Laplacian prior is used to ensure smoothness of the surface warping field. Once the atlas surface is normalized to match the range data, the internal anatomy is transformed using elastic energy minimization. We present results from performance evaluation studies of our method where we have measured the volumetric overlap between the internal organs delineated directly from MRI or CT and those estimated by our proposed warping scheme. Computed Dice coefficients indicate excellent overlap in the brain and the heart, with fair agreement in the kidneys and the bladder.

  2. Brain extraction using the watershed transform from markers

    Directory of Open Access Journals (Sweden)

    Richard eBeare

    2013-12-01

    Full Text Available Isolation of the brain from other tissue types in magnetic resonance(MR images is an important step in many types of neuro-imagingresearch using both humans and animal subjects. The importance ofbrain extraction is well appreciated - numerous approaches have beenpublished and the benefits of good extraction methods to subsequentprocessing are well known.We describe a tool - the marker based watershed scalper (MBWSS- for isolating the brain in T1-weighted MR images built usingfiltering and segmentation components from the Insight Toolkit (ITKframework. The key elements of MBWSS - the watershed transform frommarkers and aggressive filtering with large kernels - are techniquesthat have rarely been used in neuroimaging segmentation applications. MBWSSis able to reliably isolate the brain without expensive preprocessingsteps, such as registration to an atlas, and is therefore useful asthe first stage of processing pipelines. It is an informative exampleof the level of accuracy achievable without using priors in the formof atlases, shape models or libraries of examples.We validate the MBWSS using a publicly available dataset, a paediatriccohort, an adolescent cohort, intra-surgical scans and demonstrateflexibility of the approach by modifying the method to extract macaquebrains.

  3. Concordance Between Administrator and Clinician Ratings of Organizational Culture and Climate.

    Science.gov (United States)

    Beidas, Rinad S; Williams, Nathaniel J; Green, Philip D; Aarons, Gregory A; Becker-Haimes, Emily M; Evans, Arthur C; Rubin, Ronnie; Adams, Danielle R; Marcus, Steven C

    2018-01-01

    Organizational culture and climate are important determinants of behavioral health service delivery for youth. The Organizational Social Context measure is a well validated assessment of organizational culture and climate that has been developed and extensively used in public sector behavioral health service settings. The degree of concordance between administrators and clinicians in their reports of organizational culture and climate may have implications for research design, inferences, and organizational intervention. However, the extent to which administrators' and clinicians' reports demonstrate concordance is just beginning to garner attention in public behavioral health settings in the United States. We investigated the concordance between 73 administrators (i.e., supervisors, clinical directors, and executive directors) and 247 clinicians in 28 child-serving programs in a public behavioral health system. Findings suggest that administrators, compared to clinicians, reported more positive cultures and climates. Organizational size moderated this relationship such that administrators in small programs (climate in contrast to administrators in large programs (≥466 youth clients served annually) who reported more positive cultures and climates than clinicians. We propose a research agenda that examines the effect of concordance between administrators and clinicians on organizational outcomes in public behavioral health service settings.

  4. New format for ATLAS e-news

    CERN Multimedia

    Pauline Gagnon

    ATLAS e-news got a new look! As of November 30, 2007, we have a new format for ATLAS e-news. Please go to: http://atlas-service-enews.web.cern.ch/atlas-service-enews/index.html . ATLAS e-news will now be published on a weekly basis. If you are not an ATLAS colaboration member but still want to know how the ATLAS experiment is doing, we will soon have a version of ATLAS e-news intended for the general public. Information will be sent out in due time.

  5. The concordance of directly and indirectly measured built environment attributes and physical activity adoption

    Directory of Open Access Journals (Sweden)

    O'Connor Daniel P

    2011-07-01

    Full Text Available Background Physical activity (PA adoption is essential for obesity prevention and control, yet ethnic minority women report lower levels of PA and are at higher risk for obesity and its comorbidities compared to Caucasians. Epidemiological studies and ecologic models of health behavior suggest that built environmental factors are associated with health behaviors like PA, but few studies have examined the association between built environment attribute concordance and PA, and no known studies have examined attribute concordance and PA adoption. Purpose The purpose of this study was to associate the degree of concordance between directly and indirectly measured built environment attributes with changes in PA over time among African American and Hispanic Latina women participating in a PA intervention. Method Women (N = 410 completed measures of PA at Time 1 (T1 and Time 2 (T2; environmental data collected at T1 were used to compute concordance between directly and indirectly measured built environment attributes. The association between changes in PA and the degree of concordance between each directly and indirectly measured environmental attribute was assessed using repeated measures analyses. Results There were no significant associations between built environment attribute concordance values and change in self-reported or objectively measured PA. Self-reported PA significantly increased over time (F(1,184 = 7.82, p = .006, but this increase did not vary by ethnicity or any built environment attribute concordance variable. Conclusions Built environment attribute concordance may not be associated with PA changes over time among minority women. In an effort to promote PA, investigators should clarify specific built environment attributes that are important for PA adoption and whether accurate perceptions of these attributes are necessary, particularly among the vulnerable population of minority women.

  6. ATLAS Virtual Visits bringing the world into the ATLAS control room

    CERN Document Server

    AUTHOR|(CDS)2051192; The ATLAS collaboration; Yacoob, Sahal

    2016-01-01

    ATLAS Virtual Visits is a project initiated in 2011 for the Education & Outreach program of the ATLAS Experiment at CERN. Its goal is to promote public appreciation of the LHC physics program and particle physics, in general, through direct dialogue between ATLAS physicists and remote audiences. A Virtual Visit is an IP-based videoconference, coupled with a public webcast and video recording, between ATLAS physicists and remote locations around the world, that typically include high school or university classrooms, Masterclasses, science fairs, or other special events, usually hosted by collaboration members. Over the past two years, more than 10,000 people, from all of the world’s continents, have actively participated in ATLAS Virtual Visits, with many more enjoying the experience from the publicly available webcasts and recordings. We present an overview of our experience and discuss potential development for the future.

  7. A concordance-based study to assess doctors’ and nurses’ mental models in Internal Medicine

    Science.gov (United States)

    Chan, K. C. Gary; Muller-Juge, Virginie; Cullati, Stéphane; Hudelson, Patricia; Maître, Fabienne; Vu, Nu V.; Savoldelli, Georges L.; Nendaz, Mathieu R.

    2017-01-01

    Interprofessional collaboration between doctors and nurses is based on team mental models, in particular for each professional’s roles. Our objective was to identify factors influencing concordance on the expectations of doctors’ and nurses’ roles and responsibilities in an Internal Medicine ward. Using a dataset of 196 doctor-nurse pairs (14x14 = 196), we analyzed choices and prioritized management actions of 14 doctors and 14 nurses in six clinical nurse role scenarios, and in five doctor role scenarios (6 options per scenario). In logistic regression models with a non-nested correlation structure, we evaluated concordance among doctors and nurses, and adjusted for potential confounders (including prior experience in Internal Medicine, acuteness of case and gender). Concordance was associated with number of female professionals (adjusted OR 1.32, 95% CI 1.02 to 1.73), for acute situations (adjusted OR 2.02, 95% CI 1.13 to 3.62), and in doctor role scenarios (adjusted OR 2.19, 95% CI 1.32 to 3.65). Prior experience and country of training were not significant predictors of concordance. In conclusion, our concordance-based approach helped us identify areas of lower concordance in expected doctor-nurse roles and responsibilities, particularly in non-acute situations, which can be targeted by future interprofessional, educational interventions. PMID:28792524

  8. A concordance-based study to assess doctors' and nurses' mental models in Internal Medicine.

    Directory of Open Access Journals (Sweden)

    Katherine S Blondon

    Full Text Available Interprofessional collaboration between doctors and nurses is based on team mental models, in particular for each professional's roles. Our objective was to identify factors influencing concordance on the expectations of doctors' and nurses' roles and responsibilities in an Internal Medicine ward. Using a dataset of 196 doctor-nurse pairs (14x14 = 196, we analyzed choices and prioritized management actions of 14 doctors and 14 nurses in six clinical nurse role scenarios, and in five doctor role scenarios (6 options per scenario. In logistic regression models with a non-nested correlation structure, we evaluated concordance among doctors and nurses, and adjusted for potential confounders (including prior experience in Internal Medicine, acuteness of case and gender. Concordance was associated with number of female professionals (adjusted OR 1.32, 95% CI 1.02 to 1.73, for acute situations (adjusted OR 2.02, 95% CI 1.13 to 3.62, and in doctor role scenarios (adjusted OR 2.19, 95% CI 1.32 to 3.65. Prior experience and country of training were not significant predictors of concordance. In conclusion, our concordance-based approach helped us identify areas of lower concordance in expected doctor-nurse roles and responsibilities, particularly in non-acute situations, which can be targeted by future interprofessional, educational interventions.

  9. Atlas poznawczy: W stronę fundamentów wiedzy w neurokognitywistyce

    Directory of Open Access Journals (Sweden)

    Russell A. Poldrack

    2016-12-01

    Full Text Available Cognitive neuroscience aims to map mental processes onto brain function, which begs the question of what “mental processes” exist and how they relate to the tasks that are used to manipulate and measure them. This topic has been addressed informally in prior work, but we propose that cumulative progress in cognitive neuroscience requires a more systematic approach to representing the mental entities that are being mapped to brain function and the tasks used to manipulate and measure mental processes. We describe a new open collaborative project that aims to provide a knowledge base for cognitive neuroscience, called the Cognitive Atlas (accessible online at http://www.cognitiveatlas.org, and outline how this project has the potential to drive novel discoveries about both mind and brain.

  10. 76 FR 59167 - Siemens Medical Solutions USA, Inc., Oncology Care Systems Division, Concord, CA; Siemens Medical...

    Science.gov (United States)

    2011-09-23

    ... Medical Solutions USA, Inc., Oncology Care Systems Division, Concord, CA; Siemens Medical Solutions USA... Solutions USA, Inc. (Siemens), Oncology Care Systems Division, Concord, California (subject firm). The...., Oncology Care Systems Division, Concord, California (TA-W-73,158) and Siemens Medical Solutions USA, Inc...

  11. Phenotypic concordance in familial inflammatory bowel disease (IBD). Results of a nationwide IBD Spanish database.

    Science.gov (United States)

    Cabré, Eduard; Mañosa, Míriam; García-Sánchez, Valle; Gutiérrez, Ana; Ricart, Elena; Esteve, Maria; Guardiola, Jordi; Aguas, Mariam; Merino, Olga; Ponferrada, Angel; Gisbert, Javier P; Garcia-Planella, Esther; Ceña, Gloria; Cabriada, José L; Montoro, Miguel; Domènech, Eugeni

    2014-07-01

    Disease outcome has been found to be poorer in familial inflammatory bowel disease (IBD) than in sporadic forms, but assessment of phenotypic concordance in familial IBD provided controversial results. We assessed the concordance for disease type and phenotypic features in IBD families. Patients with familial IBD were identified from the IBD Spanish database ENEIDA. Families in whom at least two members were in the database were selected for concordance analysis (κ index). Concordance for type of IBD [Crohn's disease (CD) vs. ulcerative colitis (UC)], as well as for disease extent, localization and behaviour, perianal disease, extraintestinal manifestations, and indicators of severe disease (i.e., need for immunosuppressors, biological agents, and surgery) for those pairs concordant for IBD type, were analyzed. 798 out of 11,905 IBD patients (7%) in ENEIDA had familial history of IBD. Complete data of 107 families (231 patients and 144 consanguineous pairs) were available for concordance analyses. The youngest members of the pairs were diagnosed with IBD at a significantly younger age (p<0.001) than the oldest ones. Seventy-six percent of pairs matched up for the IBD type (κ=0.58; 95%CI: 0.42-0.73, moderate concordance). There was no relevant concordance for any of the phenotypic items assessed in both diseases. Familial IBD is associated with diagnostic anticipation in younger individuals. Familial history does not allow predicting any phenotypic feature other than IBD type. Copyright © 2013 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

  12. Supporting ATLAS

    CERN Multimedia

    maximilien brice

    2003-01-01

    Eighteen feet made of stainless steel will support the barrel ATLAS detector in the cavern at Point 1. In total, the ATLAS feet system will carry approximately 6000 tons, and will give the same inclination to the detector as the LHC accelerator.

  13. 101 labeled brain images and a consistent human cortical labeling protocol

    Directory of Open Access Journals (Sweden)

    Arno eKlein

    2012-12-01

    Full Text Available We introduce the Mindboggle-101 dataset, the largest and most complete set of free, publicly accessible, manually labeled human brain images. To manually label the macroscopic anatomy in magnetic resonance images of 101 healthy participants, we created a new cortical labeling protocol that relies on robust anatomical landmarks and minimal manual edits after initialization with automated labels. The Desikan-Killiany-Tourville (DKT protocol is intended to improve the ease, consistency, and accuracy of labeling human cortical areas. Given how difficult it is to label brains, the Mindboggle-101 dataset is intended to serve as brain atlases for use in labeling other brains, as a normative dataset to establish morphometric variation in a healthy population for comparison against clinical populations, and contribute to the development, training, testing, and evaluation of automated registration and labeling algorithms. To this end, we also introduce benchmarks for the evaluation of such algorithms by comparing our manual labels with labels automatically generated by probabilistic and multi-atlas registration-based approaches. All data and related software and updated information are available on the http://www.mindboggle.info/data/ website.

  14. 101 Labeled Brain Images and a Consistent Human Cortical Labeling Protocol

    Science.gov (United States)

    Klein, Arno; Tourville, Jason

    2012-01-01

    We introduce the Mindboggle-101 dataset, the largest and most complete set of free, publicly accessible, manually labeled human brain images. To manually label the macroscopic anatomy in magnetic resonance images of 101 healthy participants, we created a new cortical labeling protocol that relies on robust anatomical landmarks and minimal manual edits after initialization with automated labels. The “Desikan–Killiany–Tourville” (DKT) protocol is intended to improve the ease, consistency, and accuracy of labeling human cortical areas. Given how difficult it is to label brains, the Mindboggle-101 dataset is intended to serve as brain atlases for use in labeling other brains, as a normative dataset to establish morphometric variation in a healthy population for comparison against clinical populations, and contribute to the development, training, testing, and evaluation of automated registration and labeling algorithms. To this end, we also introduce benchmarks for the evaluation of such algorithms by comparing our manual labels with labels automatically generated by probabilistic and multi-atlas registration-based approaches. All data and related software and updated information are available on the http://mindboggle.info/data website. PMID:23227001

  15. A map of brain neuropils and fiber systems in the ant Cardiocondyla obscurior

    Directory of Open Access Journals (Sweden)

    Joris eBressan

    2015-02-01

    Full Text Available A wide spectrum of occupied ecological niches and spectacular morphological adaptations make social insects a prime object for comparative neuroanatomical studies. Eusocial insects have evolved complex societies based on caste polyphenism. A diverse behavioral repertoire of morphologically distinct castes of the same species requires a high degree of plasticity in the central nervous system. We have analyzed the central brain neuropils and fiber tract systems of the worker of the ant Cardiocondyla obscurior, a model for the study of social traits. Our analysis is based on whole mount preparations of adult brains labeled with an antibody against Drosophila-Synapsin, which cross-reacts strongly with synapses in Cardiocondyla. Neuropil compartments stand out as domains with a certain texture and intensity of the anti-Synapsin signal. By contrast, fiber tracts, which are composed of bundles of axons accompanied by glia and are devoid of synapses, appear as channels or sheaths with low anti-Synapsin signal. We have generated a digital 3D atlas of the Cardiocondyla brain neuropil. The atlas provides a reference for future studies of brain polymorphisms in distinct castes, brain development or localization of neurotransmitter systems.

  16. A map of brain neuropils and fiber systems in the ant Cardiocondyla obscurior.

    Science.gov (United States)

    Bressan, Joris M A; Benz, Martin; Oettler, Jan; Heinze, Jürgen; Hartenstein, Volker; Sprecher, Simon G

    2014-01-01

    A wide spectrum of occupied ecological niches and spectacular morphological adaptations make social insects a prime object for comparative neuroanatomical studies. Eusocial insects have evolved complex societies based on caste polyphenism. A diverse behavioral repertoire of morphologically distinct castes of the same species requires a high degree of plasticity in the central nervous system. We have analyzed the central brain neuropils and fiber tract systems of the worker of the ant Cardiocondyla obscurior, a model for the study of social traits. Our analysis is based on whole mount preparations of adult brains labeled with an antibody against Drosophila-Synapsin, which cross-reacts strongly with synapses in Cardiocondyla. Neuropil compartments stand out as domains with a certain texture and intensity of the anti-Synapsin signal. By contrast, fiber tracts, which are composed of bundles of axons accompanied by glia and are devoid of synapses, appear as channels or sheaths with low anti-Synapsin signal. We have generated a digital 3D atlas of the Cardiocondyla brain neuropil. The atlas provides a reference for future studies of brain polymorphisms in distinct castes, brain development or localization of neurotransmitter systems.

  17. Automatic segmentation of brain MRIs and mapping neuroanatomy across the human lifespan

    Science.gov (United States)

    Keihaninejad, Shiva; Heckemann, Rolf A.; Gousias, Ioannis S.; Rueckert, Daniel; Aljabar, Paul; Hajnal, Joseph V.; Hammers, Alexander

    2009-02-01

    A robust model for the automatic segmentation of human brain images into anatomically defined regions across the human lifespan would be highly desirable, but such structural segmentations of brain MRI are challenging due to age-related changes. We have developed a new method, based on established algorithms for automatic segmentation of young adults' brains. We used prior information from 30 anatomical atlases, which had been manually segmented into 83 anatomical structures. Target MRIs came from 80 subjects (~12 individuals/decade) from 20 to 90 years, with equal numbers of men, women; data from two different scanners (1.5T, 3T), using the IXI database. Each of the adult atlases was registered to each target MR image. By using additional information from segmentation into tissue classes (GM, WM and CSF) to initialise the warping based on label consistency similarity before feeding this into the previous normalised mutual information non-rigid registration, the registration became robust enough to accommodate atrophy and ventricular enlargement with age. The final segmentation was obtained by combination of the 30 propagated atlases using decision fusion. Kernel smoothing was used for modelling the structural volume changes with aging. Example linear correlation coefficients with age were, for lateral ventricular volume, rmale=0.76, rfemale=0.58 and, for hippocampal volume, rmale=-0.6, rfemale=-0.4 (allρ<0.01).

  18. Report to users of Atlas

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1996-06-01

    This report contains the following topics: Status of the ATLAS Accelerator; Highlights of Recent Research at ATLAS; Program Advisory Committee; ATLAS User Group Executive Committee; FMA Information Available On The World Wide Web; Conference on Nuclear Structure at the Limits; and Workshop on Experiments with Gammasphere at ATLAS

  19. Evaluation of an atlas-based automatic segmentation software for the delineation of brain organs at risk in a radiation therapy clinical context

    International Nuclear Information System (INIS)

    Isambert, Aurelie; Dhermain, Frederic; Bidault, Francois; Commowick, Olivier; Bondiau, Pierre-Yves; Malandain, Gregoire; Lefkopoulos, Dimitri

    2008-01-01

    Background and purpose: Conformal radiation therapy techniques require the delineation of volumes of interest, a time-consuming and operator-dependent task. In this work, we aimed to evaluate the potential interest of an atlas-based automatic segmentation software (ABAS) of brain organs at risk (OAR), when used under our clinical conditions. Materials and methods: Automatic and manual segmentations of the eyes, optic nerves, optic chiasm, pituitary gland, brain stem and cerebellum of 11 patients on T1-weighted magnetic resonance, 3-mm thick slice images were compared using the Dice similarity coefficient (DSC). The sensitivity and specificity of the ABAS were also computed and analysed from a radiotherapy point of view by splitting the ROC (Receiver Operating Characteristic) space into four sub-regions. Results: Automatic segmentation of OAR was achieved in 7-8 min. Excellent agreement was obtained between automatic and manual delineations for organs exceeding 7 cm 3 : the DSC was greater than 0.8. For smaller structures, the DSC was lower than 0.41. Conclusions: These tests demonstrated that this ABAS is a robust and reliable tool for automatic delineation of large structures under clinical conditions in our daily practice, even though the small structures must continue to be delineated manually by an expert

  20. Multi-atlas labeling with population-specific template and non-local patch-based label fusion

    DEFF Research Database (Denmark)

    Fonov, Vladimir; Coupé, Pierrick; Eskildsen, Simon Fristed

    We propose a new method combining a population-specific nonlinear template atlas approach with non-local patch-based structure segmentation for whole brain segmentation into individual structures. This way, we benefit from the efficient intensity-driven segmentation of the non-local means framework...... and from the global shape constraints imposed by the nonlinear template matching....

  1. Concordance of attachment representations in preschool siblings assessed by the attachment story completion task

    OpenAIRE

    Werner, Helene; Zahn, Salome; Titze, Karl; Walitza, Susanne; Zulauf Logoz, Marina

    2015-01-01

    Several studies have indicated only a modest concordance of attachment security in siblings in infancy. Until now, very little was known about the concordance of siblings’ attachment security beyond infancy, as assessed by the attachment story completion task. This cross-sectional study aims to examine the concordance of attachment representations of 38 first-born (4–7 years) and 38 second-born (3–5 years) siblings living in middle-class two-parent families. Personality factors and the level ...

  2. Concordance between prenatal ultrasound and autopsy findings in a tertiary center.

    Science.gov (United States)

    Rodriguez, M Angeles; Prats, Pilar; Rodríguez, Ignacio; Cusí, Victoria; Comas, Carmina

    2014-08-01

    The aim of this study was to evaluate the ultrasound (US)/autopsy concordance in elective termination of pregnancies (TOP) due to fetal causes. We performed a retrospective evaluation of elective TOP from 2004 to 2012. Inclusion criteria were gestational age at termination autopsy data. Based on the US-autopsy concordance, cases were divided into four groups: Group 1: agreement; Group 2: autopsy confirmed all US findings but provided additional information; Group 3: autopsy didn't confirm all US findings; Group 4: disagreement. One hundred and fifty-one patients fulfilled the inclusion criteria during the study period. Central nervous system malformations (91.5%), cardiovascular anomalies (90.2%) and renal system malformations (91.3%) were confirmed by autopsy. We found less concordance in the abdominal and musculoskeletal anomalies (61.5% and 66.7%, respectively). There were 130 (86%) fetuses in group 1, 7 in group 2 (4.6%), 3 in group 3 (1.9%) and 11 in group 4 (7.2%). In 5.29% of cases, the autopsy added relevant information to the diagnosis and counselling. Diagnosis concordance between US and necropsy is achieved in almost 90% of cases. An autopsy may help to adjust the diagnosis and help in counselling the parents for a future pregnancy. © 2014 John Wiley & Sons, Ltd.

  3. Stroke atlas: a 3D interactive tool correlating cerebrovascular pathology with underlying neuroanatomy and resulting neurological deficits.

    Science.gov (United States)

    Nowinski, W L; Chua, B C

    2013-02-01

    Understanding stroke-related pathology with underlying neuroanatomy and resulting neurological deficits is critical in education and clinical practice. Moreover, communicating a stroke situation to a patient/family is difficult because of complicated neuroanatomy and pathology. For this purpose, we created a stroke atlas. The atlas correlates localized cerebrovascular pathology with both the resulting disorder and surrounding neuroanatomy. It also provides 3D display both of labeled pathology and freely composed neuroanatomy. Disorders are described in terms of resulting signs, symptoms and syndromes, and they have been compiled for ischemic stroke, hemorrhagic stroke, and cerebral aneurysms. Neuroanatomy, subdivided into 2,000 components including 1,300 vessels, contains cerebrum, cerebellum, brainstem, spinal cord, white matter, deep grey nuclei, arteries, veins, dural sinuses, cranial nerves and tracts. A computer application was developed comprising: 1) anatomy browser with the normal brain atlas (created earlier); 2) simulator of infarcts/hematomas/aneurysms/stenoses; 3) tools to label pathology; 4) cerebrovascular pathology database with lesions and disorders, and resulting signs, symptoms and/or syndromes. The pathology database is populated with 70 lesions compiled from textbooks. The initial view of each pathological site is preset in terms of lesion location, size, surrounding surface and sectional neuroanatomy, and lesion and neuroanatomy labeling. The atlas is useful for medical students, residents, nurses, general practitioners, and stroke clinicians, neuroradiologists and neurologists. It may serve as an aid in patient-doctor communication helping a stroke clinician explain the situation to a patient/family. It also enables a layman to become familiarized with normal brain anatomy and understand what happens in stroke.

  4. DigiWarp: a method for deformable mouse atlas warping to surface topographic data

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, Anand A; Shattuck, David W; Toga, Arthur W [Laboratory of Neuro Imaging, UCLA School of Medicine, Los Angeles, CA 90095 (United States); Chaudhari, Abhijit J [Department of Radiology, UC Davis School of Medicine, Sacramento, CA 95817 (United States); Li Changqing; Cherry, Simon R [Department of Biomedical Engineering, University of California-Davis, Davis, CA 95616 (United States); Dutta, Joyita; Leahy, Richard M, E-mail: anand.joshi@loni.ucla.ed, E-mail: leahy@sipi.usc.ed [Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089 (United States)

    2010-10-21

    For pre-clinical bioluminescence or fluorescence optical tomography, the animal's surface topography and internal anatomy need to be estimated for improving the quantitative accuracy of reconstructed images. The animal's surface profile can be measured by all-optical systems, but estimation of the internal anatomy using optical techniques is non-trivial. A 3D anatomical mouse atlas may be warped to the estimated surface. However, fitting an atlas to surface topography data is challenging because of variations in the posture and morphology of imaged mice. In addition, acquisition of partial data (for example, from limited views or with limited sampling) can make the warping problem ill-conditioned. Here, we present a method for fitting a deformable mouse atlas to surface topographic range data acquired by an optical system. As an initialization procedure, we match the posture of the atlas to the posture of the mouse being imaged using landmark constraints. The asymmetric L{sup 2} pseudo-distance between the atlas surface and the mouse surface is then minimized in order to register two data sets. A Laplacian prior is used to ensure smoothness of the surface warping field. Once the atlas surface is normalized to match the range data, the internal anatomy is transformed using elastic energy minimization. We present results from performance evaluation studies of our method where we have measured the volumetric overlap between the internal organs delineated directly from MRI or CT and those estimated by our proposed warping scheme. Computed Dice coefficients indicate excellent overlap in the brain and the heart, with fair agreement in the kidneys and the bladder.

  5. The ATLAS Analysis Model

    CERN Multimedia

    Amir Farbin

    The ATLAS Analysis Model is a continually developing vision of how to reconcile physics analysis requirements with the ATLAS offline software and computing model constraints. In the past year this vision has influenced the evolution of the ATLAS Event Data Model, the Athena software framework, and physics analysis tools. These developments, along with the October Analysis Model Workshop and the planning for CSC analyses have led to a rapid refinement of the ATLAS Analysis Model in the past few months. This article introduces some of the relevant issues and presents the current vision of the future ATLAS Analysis Model. Event Data Model The ATLAS Event Data Model (EDM) consists of several levels of details, each targeted for a specific set of tasks. For example the Event Summary Data (ESD) stores calorimeter cells and tracking system hits thereby permitting many calibration and alignment tasks, but will be only accessible at particular computing sites with potentially large latency. In contrast, the Analysis...

  6. Preliminary Analysis Using Multi-atlas Labeling Algorithms for Tracing Longitudinal Change

    Directory of Open Access Journals (Sweden)

    Eun Young eKim

    2015-07-01

    Full Text Available Multicenter longitudinal neuroimaging has great potential to provide efficient and consistent biomarkers for research of neurodegenerative diseases and aging. In rare disease studies it is of primary importance to have a reliable tool that performs consistently for data from many different collection sites to increase study power. A multi-atlas labeling algorithm is a powerful brain image segmentation approach that is becoming increasingly popular in image processing. The present study examined the performance of multi-atlas labeling tools for subcortical identification using two types of in-vivo image database: Traveling Human Phantom and PREDICT-HD. We compared the accuracy (Dice Similarity Coefficient; DSC and intraclass correlation; ICC, multicenter reliability (Coefficient of Variance; CV, and longitudinal reliability (volume trajectory smoothness and Akaike Information Criterion; AIC of three automated segmentation approaches: two multi-atlas labeling tools, MABMIS and MALF, and a machine-learning-based tool, BRAINSCut. In general, MALF showed the best performance (higher DSC, ICC, lower CV, AIC, and smoother trajectory with a couple of exceptions. First, the results of accumben, where BRAINSCut showed higher reliability, were still premature to discuss their reliability levels since their validity is still in doubt (DSC<0.7, ICC < 0.7. For caudate, BRAINSCut presented slightly better accuracy while MALF showed significantly smoother longitudinal trajectory. We discuss advantages and limitations of these performance variations and conclude that improved segmentation quality can be achieved using multi-atlas labeling methods. While multi-atlas labeling methods are likely to help improve overall segmentation quality, caution has to be taken when one chooses an approach, as our results suggest that segmentation outcome can vary depending on research interest.

  7. Brain parenchymal damage in neuromyelitis optica spectrum disorder - A multimodal MRI study

    Energy Technology Data Exchange (ETDEWEB)

    Pache, F.; Paul, F. [Max Delbrueck Center for Molecular Medicine and Charite Universitaetsmedizin Berlin, NeuroCure Clinical Research Center and Experimental and Clinical Research Center, Berlin (Germany); Charite Universitaetsmedizin Berlin, Department of Neurology, Berlin (Germany); Zimmermann, H.; Lacheta, A.; Papazoglou, S.; Kuchling, J.; Wuerfel, J.; Brandt, A.U. [Max Delbrueck Center for Molecular Medicine and Charite Universitaetsmedizin Berlin, NeuroCure Clinical Research Center and Experimental and Clinical Research Center, Berlin (Germany); Finke, C. [Charite Universitaetsmedizin Berlin, Department of Neurology, Berlin (Germany); Humboldt-Universitaet zu Berlin, Berlin School of Mind and Brain, Berlin (Germany); Hamm, B. [Charite Universitaetsmedizin Berlin, Department of Radiology, Berlin (Germany); Ruprecht, K. [Charite Universitaetsmedizin Berlin, Department of Neurology, Berlin (Germany); Scheel, M. [Max Delbrueck Center for Molecular Medicine and Charite Universitaetsmedizin Berlin, NeuroCure Clinical Research Center and Experimental and Clinical Research Center, Berlin (Germany); Charite Universitaetsmedizin Berlin, Department of Radiology, Berlin (Germany)

    2016-12-15

    To investigate different brain regions for grey (GM) and white matter (WM) damage in a well-defined cohort of neuromyelitis optica spectrum disorder (NMOSD) patients and compare advanced MRI techniques (VBM, Subcortical and cortical analyses (Freesurfer), and DTI) for their ability to detect damage in NMOSD. We analyzed 21 NMOSD patients and 21 age and gender matched control subjects. VBM (GW/WM) and DTI whole brain (TBSS) analyses were performed at different statistical thresholds to reflect different statistical approaches in previous studies. In an automated atlas-based approach, Freesurfer and DTI results were compared between NMOSD and controls. DTI TBSS and DTI atlas based analysis demonstrated microstructural impairment only within the optic radiation or in regions associated with the optic radiation (posterior thalamic radiation p < 0.001, 6.9 % reduction of fractional anisotropy). VBM demonstrated widespread brain GM and WM reduction, but only at exploratory statistical thresholds, with no differences remaining after correction for multiple comparisons. Freesurfer analysis demonstrated no group differences. NMOSD specific parenchymal brain damage is predominantly located in the optic radiation, likely due to a secondary degeneration caused by ON. In comparison, DTI appears to be the most reliable and sensitive technique for brain damage detection in NMOSD. (orig.)

  8. Brain parenchymal damage in neuromyelitis optica spectrum disorder - A multimodal MRI study

    International Nuclear Information System (INIS)

    Pache, F.; Paul, F.; Zimmermann, H.; Lacheta, A.; Papazoglou, S.; Kuchling, J.; Wuerfel, J.; Brandt, A.U.; Finke, C.; Hamm, B.; Ruprecht, K.; Scheel, M.

    2016-01-01

    To investigate different brain regions for grey (GM) and white matter (WM) damage in a well-defined cohort of neuromyelitis optica spectrum disorder (NMOSD) patients and compare advanced MRI techniques (VBM, Subcortical and cortical analyses (Freesurfer), and DTI) for their ability to detect damage in NMOSD. We analyzed 21 NMOSD patients and 21 age and gender matched control subjects. VBM (GW/WM) and DTI whole brain (TBSS) analyses were performed at different statistical thresholds to reflect different statistical approaches in previous studies. In an automated atlas-based approach, Freesurfer and DTI results were compared between NMOSD and controls. DTI TBSS and DTI atlas based analysis demonstrated microstructural impairment only within the optic radiation or in regions associated with the optic radiation (posterior thalamic radiation p < 0.001, 6.9 % reduction of fractional anisotropy). VBM demonstrated widespread brain GM and WM reduction, but only at exploratory statistical thresholds, with no differences remaining after correction for multiple comparisons. Freesurfer analysis demonstrated no group differences. NMOSD specific parenchymal brain damage is predominantly located in the optic radiation, likely due to a secondary degeneration caused by ON. In comparison, DTI appears to be the most reliable and sensitive technique for brain damage detection in NMOSD. (orig.)

  9. A Generative Probabilistic Model and Discriminative Extensions for Brain Lesion Segmentation - With Application to Tumor and Stroke

    DEFF Research Database (Denmark)

    Menze, Bjoern H.; Van Leemput, Koen; Lashkari, Danial

    2016-01-01

    jointly from the image data. It delineates lesion areas individually in each channel, allowing for differences in lesion appearance across modalities, an important feature of many brain tumor imaging sequences. We also propose discriminative model extensions to map the output of the generative model......), to estimate the label map for a new image. Our model augments the probabilistic atlas of the healthy tissues with a latent atlas of the lesion. We derive an estimation algorithm with closed-form EM update equations. The method extracts a latent atlas prior distribution and the lesion posterior distributions...

  10. ATLAS Distributed Computing

    CERN Document Server

    Schovancova, J; The ATLAS collaboration

    2011-01-01

    The poster details the different aspects of the ATLAS Distributed Computing experience after the first year of LHC data taking. We describe the performance of the ATLAS distributed computing system and the lessons learned during the 2010 run, pointing out parts of the system which were in a good shape, and also spotting areas which required improvements. Improvements ranged from hardware upgrade on the ATLAS Tier-0 computing pools to improve data distribution rates, tuning of FTS channels between CERN and Tier-1s, and studying data access patterns for Grid analysis to improve the global processing rate. We show recent software development driven by operational needs with emphasis on data management and job execution in the ATLAS production system.

  11. Individual Identification Using Functional Brain Fingerprint Detected by Recurrent Neural Network.

    Science.gov (United States)

    Chen, Shiyang; Hu, Xiaoping P

    2018-03-20

    Individual identification based on brain function has gained traction in literature. Investigating individual differences in brain function can provide additional insights into the brain. In this work, we introduce a recurrent neural network based model for identifying individuals based on only a short segment of resting state functional MRI data. In addition, we demonstrate how the global signal and differences in atlases affect the individual identifiability. Furthermore, we investigate neural network features that exhibit the uniqueness of each individual. The results indicate that our model is able to identify individuals based on neural features and provides additional information regarding brain dynamics.

  12. Guideline concordance of treatment for depressive disorders in Canada.

    Science.gov (United States)

    Duhoux, Arnaud; Fournier, Louise; Nguyen, Cat Tuong; Roberge, Pasquale; Beveridge, Rachelle

    2009-05-01

    Depression is one of the most prevalent mental health problems worldwide with considerable social and economic burdens. While practice guidelines exist, their adherence is inconsistent in clinical practice. To provide up-to-date national estimates of the adequacy of treatment received by Canadians having suffered a major depressive disorder (MDD) and examine factors associated with this adequacy. To evaluate the impact of different definitions of guideline-concordant treatment on the results. Data were drawn from the Canadian Community Health Survey, cycle 1.2: Mental Health and Well-Being (CCHS 1.2), a nationally representative survey conducted in 2002 and targetting persons aged 15 years or older living in private dwellings. In order to calculate the prevalence of treatment adequacy, we used a sample of 1,563 individuals meeting the criteria for MDD in the 12 months preceding the survey. A subset of 831 subjects who reported having used health services for mental health purposes at least once during that time served to identify the factors associated with treatment adequacy. Four definitions of minimally adequate treatment were considered and covariates were selected according to a well-known behavioral model. The analyses consisted of prevalence estimates and logistic regression models. Among selected subjects, 55% received guideline-concordant treatment according to the Canadian guidelines. Inadequacy was more prevalent in rural settings, for less complex cases, and in the general medical sector. Depending on the definition, prevalence of guideline-concordant treatment ranged between 48 and 71%, and factors associated with guideline-concordant treatment were mainly need factors and sector of care. A large proportion of people with a depressive disorder do not receive minimally adequate treatment. Improved access to and quality of treatment is required, especially in primary care settings.

  13. ATLAS Review Office

    CERN Multimedia

    Szeless, B

    The ATLAS internal reviews, be it the mandatory Production Readiness Reviews, the now newly installed Production Advancement Reviews, or the more and more requested different Design Reviews, have become a part of our ATLAS culture over the past years. The Activity Systems Status Overviews are, for the time being, a one in time event and should be held for each system as soon as possible to have some meaning. There seems to a consensus that the reviews have become a useful project tool for the ATLAS management but even more so for the sub-systems themselves making achievements as well as possible shortcomings visible. One other recognized byproduct is the increasing cross talk between the systems, a very important ingredient to make profit all the systems from the large collective knowledge we dispose of in ATLAS. In the last two months, the first two PARs were organized for the MDT End Caps and the TRT Barrel Modules, both part of the US contribution to the ATLAS Project. Furthermore several different design...

  14. Berliner Philarmoniker ATLAS visit

    CERN Multimedia

    ATLAS Collaboration

    2017-01-01

    The Berliner Philarmoniker in on tour through Europe. They stopped on June 27th in Geneva, for a concert at the Victoria Hall. An ATLAS visit was organised the morning after, lead by the ATLAS spokesperson Karl Jakobs (welcome and overview talk) and two ATLAS guides (AVC visit and 3D movie).

  15. Waxholm space: an image-based reference for coordinating mouse brain research.

    Science.gov (United States)

    Johnson, G Allan; Badea, Alexandra; Brandenburg, Jeffrey; Cofer, Gary; Fubara, Boma; Liu, Song; Nissanov, Jonathan

    2010-11-01

    We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 mum (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing. All the data is available for download via the web. Copyright 2010 Elsevier Inc. All rights reserved.

  16. Negative concord and the scope of universals

    NARCIS (Netherlands)

    Giannakidou, A

    2000-01-01

    In this paper, I propose an analysis of Greek negative concord (NC) in terms of quantifier scope. It is shown that there is no evidence that Greek NC n-words are indefinites or negative quantifiers, NC n-words are analysed as universal quantifiers, which are sensitive to negative polarity, and which

  17. Concord Grape Juice Supplementation Improves Memory Function In Older Adults with Mild Cognitive Impairment

    Science.gov (United States)

    Concord grape juice contains flavonoid polyphenol compounds, which have antioxidant and anti-inflammatory properties and influence neuronal signaling. Concord grape juice supplementation has been shown to reduce inflammation, blood pressure, and vascular pathology in individuals with cardiovascular...

  18. Software Validation in ATLAS

    International Nuclear Information System (INIS)

    Hodgkinson, Mark; Seuster, Rolf; Simmons, Brinick; Sherwood, Peter; Rousseau, David

    2012-01-01

    The ATLAS collaboration operates an extensive set of protocols to validate the quality of the offline software in a timely manner. This is essential in order to process the large amounts of data being collected by the ATLAS detector in 2011 without complications on the offline software side. We will discuss a number of different strategies used to validate the ATLAS offline software; running the ATLAS framework software, Athena, in a variety of configurations daily on each nightly build via the ATLAS Nightly System (ATN) and Run Time Tester (RTT) systems; the monitoring of these tests and checking the compilation of the software via distributed teams of rotating shifters; monitoring of and follow up on bug reports by the shifter teams and periodic software cleaning weeks to improve the quality of the offline software further.

  19. ATLAS Open Data project

    CERN Document Server

    The ATLAS collaboration

    2018-01-01

    The current ATLAS model of Open Access to recorded and simulated data offers the opportunity to access datasets with a focus on education, training and outreach. This mandate supports the creation of platforms, projects, software, and educational products used all over the planet. We describe the overall status of ATLAS Open Data (http://opendata.atlas.cern) activities, from core ATLAS activities and releases to individual and group efforts, as well as educational programs, and final web or software-based (and hard-copy) products that have been produced or are under development. The relatively large number and heterogeneous use cases currently documented is driving an upcoming release of more data and resources for the ATLAS Community and anyone interested to explore the world of experimental particle physics and the computer sciences through data analysis.

  20. AGIS: The ATLAS Grid Information System

    CERN Document Server

    Anisenkov, A; The ATLAS collaboration; Klimentov, A; Senchenko, A

    2012-01-01

    The ATLAS Computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we present ATLAS Grid Information System (AGIS) designed to integrate configuration and status information about resources, services and topology of whole ATLAS Grid needed by ATLAS Distributed Computing applications and services.

  1. Cartea de Colorat a Experimentului ATLAS - ATLAS Experiment Colouring Book in Romanian

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    Language: Romanian - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration. Limba: Română - Cartea de Colorat a Experimentului ATLAS este o carte educativă gratuită, ideală pentru copiii cu vârsta cuprinsă între 5-9 ani. Scopul său este de a introduce copii în domeniul fizicii de înaltă energie, precum și activitatea desfășurată de colaborarea ATLAS.

  2. Grading of Cerebral Glioma with Multiparametric MR Imaging and {sup 18}F-FDG-PET: Concordance and Accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jeong Hee; Kim, Ji-hoon; Sohn, Chul-Ho; Choi, Seung Hong; Yun, Tae Jin; Song, Yong Sub [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Kang, Won Jun [Seoul National University Hospital, Department of Nuclear Medicine, Seoul (Korea, Republic of); Yonsei University College of Medicine, Department of Nuclear Medicine, Seoul (Korea, Republic of); Eun, Yong [Seoul National University, College of Medicine, Seoul (Korea, Republic of); Chang, Kee-Hyun [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Soonchunhyang University Bucheon Hospital, Department of Radiology, Bucheon (Korea, Republic of)

    2014-02-15

    To retrospectively evaluate concordance rates and predictive values in concordant cases among multiparametric MR techniques and FDG-PET to grade cerebral gliomas. Multiparametric MR imaging and FDG-PET were performed in 60 consecutive patients with cerebral gliomas (12 low-grade and 48 high-grade gliomas). As the dichotomic variables, conventional MRI, minimum apparent diffusion coefficient in diffusion-weighted imaging, maximum relative cerebral blood volume ratio in perfusion-weighted imaging, choline/creatine ratio and (lipid and lactate)/creatine ratio in MR spectroscopy, and maximum standardised uptake value ratio in FDG-PET in low- and high-grade gliomas were compared. Their concordance rates and positive/negative predictive values (PPV/NPV) in concordant cases were obtained for the various combinations of multiparametric MR techniques and FDG-PET. There were significant differences between low- and high-grade gliomas in all techniques. Combinations of two, three, four, and five out of the five techniques showed concordance rates of 77.0 ± 4.8 %, 65.5 ± 4.0 %, 58.3 ± 2.6 % and 53.3 %, PPV in high-grade concordant cases of 97.3 ± 1.7 %, 99.1 ± 1.4 %, 100.0 ± 0 % and 100.0 % and NPV in low-grade concordant cases of 70.2 ± 7.5 %, 78.0 ± 6.0 %, 80.3 ± 3.4 % and 80.0 %, respectively. Multiparametric MR techniques and FDG-PET have a concordant tendency in a two-tiered classification for the grading of cerebral glioma. If at least two examinations concordantly indicated high-grade gliomas, the PPV was about 95 %. (orig.)

  3. Atlas-based functional radiosurgery: Early results

    Energy Technology Data Exchange (ETDEWEB)

    Stancanello, J.; Romanelli, P.; Pantelis, E.; Sebastiano, F.; Modugno, N. [Politecnico di Milano, Bioengineering Department and NEARlab, Milano, 20133 (Italy) and Siemens AG, Research and Clinical Collaborations, Erlangen, 91052 (Germany); Functional Neurosurgery Deptartment, Neuromed IRCCS, Pozzilli, 86077 (Italy); CyberKnife Center, Iatropolis, Athens, 15231 (Greece); Functional Neurosurgery Deptartment, Neuromed IRCCS, Pozzilli, 86077 (Italy)

    2009-02-15

    Functional disorders of the brain, such as dystonia and neuropathic pain, may respond poorly to medical therapy. Deep brain stimulation (DBS) of the globus pallidus pars interna (GPi) and the centromedian nucleus of the thalamus (CMN) may alleviate dystonia and neuropathic pain, respectively. A noninvasive alternative to DBS is radiosurgical ablation [internal pallidotomy (IP) and medial thalamotomy (MT)]. The main technical limitation of radiosurgery is that targets are selected only on the basis of MRI anatomy, without electrophysiological confirmation. This means that, to be feasible, image-based targeting must be highly accurate and reproducible. Here, we report on the feasibility of an atlas-based approach to targeting for functional radiosurgery. In this method, masks of the GPi, CMN, and medio-dorsal nucleus were nonrigidly registered to patients' T1-weighted MRI (T1w-MRI) and superimposed on patients' T2-weighted MRI (T2w-MRI). Radiosurgical targets were identified on the T2w-MRI registered to the planning CT by an expert functional neurosurgeon. To assess its feasibility, two patients were treated with the CyberKnife using this method of targeting; a patient with dystonia received an IP (120 Gy prescribed to the 65% isodose) and a patient with neuropathic pain received a MT (120 Gy to the 77% isodose). Six months after treatment, T2w-MRIs and contrast-enhanced T1w-MRIs showed edematous regions around the lesions; target placements were reevaluated by DW-MRIs. At 12 months post-treatment steroids for radiation-induced edema and medications for dystonia and neuropathic pain were suppressed. Both patients experienced significant relief from pain and dystonia-related problems. Fifteen months after treatment edema had disappeared. Thus, this work shows promising feasibility of atlas-based functional radiosurgery to improve patient condition. Further investigations are indicated for optimizing treatment dose.

  4. Spousal Concordance of Diabetes Mellitus among Women in Ajman, United Arab Emirates.

    Science.gov (United States)

    Al-Sharbatti, Shatha S; Abed, Yasmeen I; Al-Heety, Lujain M; Basha, Shaikh A

    2016-05-01

    Spousal concordance is defined as similar behaviours and associated health statuses between spouses. This study aimed to identify the concordance of diabetes mellitus (DM) and related variables among genetically unrelated couples in Ajman, United Arab Emirates (UAE). This cross-sectional study included 270 married women attending either the Mushairef Health Center or the Gulf Medical College Hospital in Ajman between May and November 2012. A validated questionnaire was designed to determine sociodemographic characteristics and a history or family history of DM, hypertension, coronary artery disease or dyslipidaemia among the women and their husbands. The weight, height, body mass index, waist circumference, fasting blood sugar and glycated haemoglobin (HbA1c) levels of all women were measured. Of the women, 39.3% of those with diabetic husbands and 39.9% of those with non-diabetic husbands were diabetic themselves (P >0.050). The prevalence of DM spousal concordance was 17.8%. A history of hypertension, coronary artery disease and dyslipidaemia was significantly more frequent among women whose husbands had a history of the same conditions (P = 0.001, 0.040 and 0.002, respectively). Spousal concordance of abnormal glycaemia among non-diabetic women with diabetic husbands was significant (P = 0.001). Having a diabetic husband (P = 0.006) and being obese (P = 0.009) were the only significant predictors of hyperglycaemia among non-diabetic women after controlling for confounding factors. There was significant concordance of abnormal glycaemia among non-diabetic women with diabetic husbands. The spouses of diabetic patients may therefore be a target population for regular hyperglycaemia and DM screening.

  5. AGIS: The ATLAS Grid Information System

    CERN Document Server

    Anisenkov, Alexey; Di Girolamo, Alessandro; Gayazov, Stavro; Klimentov, Alexei; Oleynik, Danila; Senchenko, Alexander

    2012-01-01

    ATLAS is a particle physics experiment at the Large Hadron Collider at CERN. The experiment produces petabytes of data annually through simulation production and tens petabytes of data per year from the detector itself. The ATLAS Computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we present ATLAS Grid Information System (AGIS) designed to integrate configuration and status information about resources, services and topology of whole ATLAS Grid needed by ATLAS Distributed Computing applications and services.

  6. Learning-by-Concordance (LbC): introducing undergraduate students to the complexity and uncertainty of clinical practice.

    Science.gov (United States)

    Fernandez, Nicolas; Foucault, Amélie; Dubé, Serge; Robert, Diane; Lafond, Chantal; Vincent, Anne-Marie; Kassis, Jeannine; Kazitani, Driss; Charlin, Bernard

    2016-10-01

    A current challenge in medical education is the steep exposure to the complexity and uncertainty of clinical practice in early clerkship. The gap between pre-clinical courses and the reality of clinical decision-making can be overwhelming for undergraduate students. The Learning-by-Concordance (LbC) approach aims to bridge this gap by embedding complexity and uncertainty by relying on real-life situations and exposure to expert reasoning processes to support learning. LbC provides three forms of support: 1) expert responses that students compare with their own, 2) expert explanations and 3) recognized scholars' key-messages. Three different LbC inspired learning tools were used by 900 undergraduate medical students in three courses: Concordance-of-Reasoning in a 1 st -year hematology course; Concordance-of-Perception in a 2nd-year pulmonary physio-pathology course, and; Concordance-of-Professional-Judgment with 3rd-year clerkship students. Thematic analysis was conducted on freely volunteered qualitative comments provided by 404 students. Absence of a right answer was challenging for 1 st year concordance-of-reasoning group; the 2 nd year visual concordance group found radiology images initially difficult and unnerving and the 3 rd year concordance-of-judgment group recognized the importance of divergent expert opinion. Expert panel answers and explanations constitute an example of "cognitive apprenticeship" that could contribute to the development of appropriate professional reasoning processes.

  7. An in vivo three-dimensional magnetic resonance imaging-based averaged brain collection of the neonatal piglet (Sus scrofa.

    Directory of Open Access Journals (Sweden)

    Matthew S Conrad

    Full Text Available Due to the fact that morphology and perinatal growth of the piglet brain is similar to humans, use of the piglet as a translational animal model for neurodevelopmental studies is increasing. Magnetic resonance imaging (MRI can be a powerful tool to study neurodevelopment in piglets, but many of the MRI resources have been produced for adult humans. Here, we present an average in vivo MRI-based atlas specific for the 4-week-old piglet. In addition, we have developed probabilistic tissue classification maps. These tools can be used with brain mapping software packages (e.g. SPM and FSL to aid in voxel-based morphometry and image analysis techniques. The atlas enables efficient study of neurodevelopment in a highly tractable translational animal with brain growth and development similar to humans.

  8. Wind Atlas for Egypt

    DEFF Research Database (Denmark)

    The results of a comprehensive, 8-year wind resource assessment programme in Egypt are presented. The objective has been to provide reliable and accurate wind atlas data sets for evaluating the potential wind power output from large electricityproducing wind turbine installations. The regional wind...... climates of Egypt have been determined by two independent methods: a traditional wind atlas based on observations from more than 30 stations all over Egypt, and a numerical wind atlas based on long-term reanalysis data and a mesoscale model (KAMM). The mean absolute error comparing the two methods is about...... 10% for two large-scale KAMM domains covering all of Egypt, and typically about 5% for several smaller-scale regional domains. The numerical wind atlas covers all of Egypt, whereas the meteorological stations are concentrated in six regions. The Wind Atlas for Egypt represents a significant step...

  9. Wind Atlas for Egypt

    DEFF Research Database (Denmark)

    Mortensen, Niels Gylling; Said Said, Usama; Badger, Jake

    2006-01-01

    The results of a comprehensive, 8-year wind resource assessment programme in Egypt are presented. The objective has been to provide reliable and accurate wind atlas data sets for evaluating the potential wind power output from large electricityproducing wind turbine installations. The regional wind...... climates of Egypt have been determined by two independent methods: a traditional wind atlas based on observations from more than 30 stations all over Egypt, and a numerical wind atlas based on long-term reanalysis data and a mesoscale model (KAMM). The mean absolute error comparing the two methods is about...... 10% for two large-scale KAMM domains covering all of Egypt, and typically about 5% for several smaller-scale regional domains. The numerical wind atlas covers all of Egypt, whereas the meteorological stations are concentrated in six regions. The Wind Atlas for Egypt represents a significant step...

  10. Recent ATLAS Articles on WLAP

    CERN Multimedia

    Goldfarb, S.

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: June ATLAS Plenary Meeting Tutorial on Physics EDM and Tools (June) Freiburg Overview Week Ketevi Assamagan's Tutorial on Analysis Tools Click here to browse WLAP for all ATLAS lectures.

  11. File list: Pol.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Neu.05.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.05.AllAg.Brain.bed ...

  12. File list: Pol.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Neu.50.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.50.AllAg.Brain.bed ...

  13. File list: Pol.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Neu.10.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.10.AllAg.Brain.bed ...

  14. File list: Pol.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Pol.Neu.20.AllAg.Brain mm9 RNA polymerase Neural Brain SRX236085,ERX132833,SRX01708...2,SRX680480,SRX020249 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Pol.Neu.20.AllAg.Brain.bed ...

  15. Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

    International Nuclear Information System (INIS)

    Bouchami, J; Dallaire, F; Gutierrez, A; Idarraga, J; Leroy, C; Picard, S; Scallon, O; Kral, V; PospIsil, S; Solc, J; Suk, M; Turecek, D; Vykydal, Z; Zemlieka, J

    2011-01-01

    The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of 6 LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) - based on the ROOT application - allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons ( 252 Cf and 241 AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

  16. File list: His.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.05.AllAg.Brain mm9 Histone Neural Brain SRX680482,SRX017084,SRX680481,SRX21...9253,SRX680484,SRX680483,SRX680485 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.05.AllAg.Brain.bed ...

  17. File list: His.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.50.AllAg.Brain mm9 Histone Neural Brain SRX680482,SRX219253,SRX680484,SRX68...0485,SRX680483,SRX017084,SRX680481 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.50.AllAg.Brain.bed ...

  18. File list: His.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.20.AllAg.Brain mm9 Histone Neural Brain SRX680482,SRX219253,SRX680484,SRX68...0481,SRX680485,SRX017084,SRX680483 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.20.AllAg.Brain.bed ...

  19. File list: His.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.10.AllAg.Brain mm9 Histone Neural Brain SRX680482,SRX680481,SRX219253,SRX68...0484,SRX680485,SRX017084,SRX680483 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/His.Neu.10.AllAg.Brain.bed ...

  20. A Place Called Home: Educational Reform in a Concord, Massachusetts School, 1897-1914

    Science.gov (United States)

    Morice, Linda C.

    2012-01-01

    This paper examines the role of place in the reform efforts of two teachers who established Miss White's Home School in Concord, Massachusetts (USA). Flora and Mary White rebelled against the prevailing industrial model of instruction in tax-supported schools where they taught. As a solution, they moved to Concord--a nonconformist town with a…

  1. The brain MRI classification problem from wavelets perspective

    Science.gov (United States)

    Bendib, Mohamed M.; Merouani, Hayet F.; Diaba, Fatma

    2015-02-01

    Haar and Daubechies 4 (DB4) are the most used wavelets for brain MRI (Magnetic Resonance Imaging) classification. The former is simple and fast to compute while the latter is more complex and offers a better resolution. This paper explores the potential of both of them in performing Normal versus Pathological discrimination on the one hand, and Multiclassification on the other hand. The Whole Brain Atlas is used as a validation database, and the Random Forest (RF) algorithm is employed as a learning approach. The achieved results are discussed and statistically compared.

  2. Corpus-aided language pedagogy : the use of concordance lines in vocabulary instruction

    OpenAIRE

    Kazaz, İlknur

    2015-01-01

    Ankara : The Program of Teaching English as a Foreign Language Bilkent University, 2015. Thesis (Master's) -- Bilkent University, 2015. Includes bibliographical references leaves 83-91. This study investigated the effectiveness of the use of a concordance software and concordance lines as a pedagogical tool to learn the target vocabulary of a text book. The purpose of the study was to compare the effects of corpus-aided vocabulary instruction with traditional vocabulary teac...

  3. Where Do Self-Concordant Goals Come From? The Role of Domain-Specific Psychological Need Satisfaction.

    Science.gov (United States)

    Milyavskaya, Marina; Nadolny, Daniel; Koestner, Richard

    2014-06-01

    Previous research has shown that self-concordant goals are more likely to be attained. But what leads someone to adopt a self-concordant goal in the first place? The present research addresses this question by looking at the domains in which goals are set, focusing on the amount of psychological need satisfaction experienced in these domains. Across three experimental studies, we demonstrate that domain-related need satisfaction predicts the extent to which people adopt self-concordant goals in a given domain, laying the foundation for successful goal pursuit. In addition, we show that need satisfaction influences goal self-concordance because in need-satisfying domains people are both more likely to choose the most self-concordant goal (among a set of comparable choices), and are more likely to internalize the possible goals. The implications of this research for goal setting and pursuit as well as for the importance of examining goals within their broader motivational framework are discussed. © 2014 by the Society for Personality and Social Psychology, Inc.

  4. Exosomal biomarkers of brain insulin resistance associated with regional atrophy in Alzheimer's disease.

    Science.gov (United States)

    Mullins, Roger J; Mustapic, Maja; Goetzl, Edward J; Kapogiannis, Dimitrios

    2017-04-01

    Brain insulin resistance (IR), which depends on insulin-receptor-substrate-1 (IRS-1) phosphorylation, is characteristic of Alzheimer's disease (AD). Previously, we demonstrated higher pSer312-IRS-1 (ineffective insulin signaling) and lower p-panTyr-IRS-1 (effective insulin signaling) in neural origin-enriched plasma exosomes of AD patients vs. Here, we hypothesized that these exosomal biomarkers associate with brain atrophy in AD. We studied 24 subjects with biomarker-supported probable AD (low CSF Aβ 42 ). Exosomes were isolated from plasma, enriched for neural origin using immunoprecipitation for L1CAM, and measured for pSer 312 - and p-panTyr-IRS-1 phosphotypes. MPRAGE images were segmented by brain tissue type and voxel-based morphometry (VBM) analysis for gray matter against pSer 312 - and p-panTyr-IRS-1 was conducted. Given the regionally variable brain expression of IRS-1, we used the Allen Brain Atlas to make spatial comparisons between VBM results and IRS-1 expression. Brain volume was positively associated with P-panTyr-IRS-1 and negatively associated with pSer 312 -IRS-1 in a strikingly similar regional pattern (bilateral parietal-occipital junction, R middle temporal gyrus). This volumetric association pattern was spatially correlated with Allen Human Brain atlas normal brain IRS-1 expression. Exosomal biomarkers of brain IR are thus associated with atrophy in AD as could be expected by their pathophysiological roles and do so in a pattern that reflects regional IRS-1 expression. Furthermore, neural-origin plasma exosomes may recover molecular signals from specific brain regions. Hum Brain Mapp 38:1933-1940, 2017. © 2017 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  5. Fast, Sequence Adaptive Parcellation of Brain MR Using Parametric Models

    DEFF Research Database (Denmark)

    Puonti, Oula; Iglesias, Juan Eugenio; Van Leemput, Koen

    2013-01-01

    In this paper we propose a method for whole brain parcellation using the type of generative parametric models typically used in tissue classification. Compared to the non-parametric, multi-atlas segmentation techniques that have become popular in recent years, our method obtains state-of-the-art ...

  6. ATLAS@Home looks for CERN volunteers

    CERN Multimedia

    Rosaria Marraffino

    2014-01-01

    ATLAS@Home is a CERN volunteer computing project that runs simulated ATLAS events. As the project ramps up, the project team is looking for CERN volunteers to test the system before planning a bigger promotion for the public.   The ATLAS@home outreach website. ATLAS@Home is a large-scale research project that runs ATLAS experiment simulation software inside virtual machines hosted by volunteer computers. “People from all over the world offer up their computers’ idle time to run simulation programmes to help physicists extract information from the large amount of data collected by the detector,” explains Claire Adam Bourdarios of the ATLAS@Home project. “The ATLAS@Home project aims to extrapolate the Standard Model at a higher energy and explore what new physics may look like. Everything we’re currently running is preparation for next year's run.” ATLAS@Home became an official BOINC (Berkeley Open Infrastructure for Network ...

  7. File list: Oth.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Neu.05.AllAg.Brain mm9 TFs and others Neural Brain SRX661585,ERX450950,ERX33906...ERX1027837,ERX370082,ERX370085,ERX370083,ERX370084 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Neu.05.AllAg.Brain.bed ...

  8. File list: Oth.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Neu.50.AllAg.Brain mm9 TFs and others Neural Brain SRX661585,SRX116258,SRX11625...,ERX370082,ERX370083,ERX370085,ERX370084,SRX150260 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Neu.50.AllAg.Brain.bed ...

  9. File list: Oth.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Neu.20.AllAg.Brain mm9 TFs and others Neural Brain SRX661585,SRX116258,SRX01708...,SRX150260,ERX370082,ERX370083,ERX370085,ERX370084 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Neu.20.AllAg.Brain.bed ...

  10. File list: Oth.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Oth.Neu.10.AllAg.Brain mm9 TFs and others Neural Brain SRX661585,SRX093164,SRX11625...,ERX339067,ERX370082,ERX370083,ERX370085,ERX370084 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Oth.Neu.10.AllAg.Brain.bed ...

  11. Implementation of the ATLAS trigger within the ATLAS Multi­Threaded Software Framework AthenaMT

    CERN Document Server

    Wynne, Benjamin; The ATLAS collaboration

    2016-01-01

    We present an implementation of the ATLAS High Level Trigger that provides parallel execution of trigger algorithms within the ATLAS multi­threaded software framework, AthenaMT. This development will enable the ATLAS High Level Trigger to meet future challenges due to the evolution of computing hardware and upgrades of the Large Hadron Collider, LHC, and ATLAS Detector. During the LHC data­taking period starting in 2021, luminosity will reach up to three times the original design value. Luminosity will increase further, to up to 7.5 times the design value, in 2026 following LHC and ATLAS upgrades. This includes an upgrade of the ATLAS trigger architecture that will result in an increase in the High Level Trigger input rate by a factor of 4 to 10 compared to the current maximum rate of 100 kHz. The current ATLAS multiprocess framework, AthenaMP, manages a number of processes that process events independently, executing algorithms sequentially in each process. AthenaMT will provide a fully multi­threaded env...

  12. Concord, Convergence and Accommodation in Bilingual Children

    Science.gov (United States)

    Radford, Andrew; Kupisch, Tanja; Koppe, Regina; Azzaro, Gabriele

    2007-01-01

    This paper examines the syntax of "GENDER CONCORD" in mixed utterances where bilingual children switch between a modifier in one language and a noun in another. Particular attention is paid to how children deal with potential gender mismatches between modifier and noun, i.e., if one of the languages has grammatical gender but the other does not,…

  13. Correlates of and couples' concordance in reports of recent sexual behavior and contraceptive use.

    Science.gov (United States)

    Koffi, Alain K; Adjiwanou, Visseho D; Becker, Stan; Olaolorun, Funmilola; Tsui, Amy O

    2012-03-01

    This study uses couple-level data to measure couples' concordance of self-reported time since last coitus and of condom and other contraceptive use at last sexual intercourse among monogamous couples in Liberia (N = 1,673), Madagascar (N = 4,138), and Namibia (N = 588). The study also examines the characteristics associated with sexual behavior and contraceptive use occurring in the 28 days prior to the interviews among couples whose reports are concordant. Overall, our study finds less than 75 percent concordance in reporting of time since last coitus. Use of condoms and other contraceptives yielded fair (0.27) to substantial (0.67) agreement on the kappa index. Factors predicting a shorter time since last coitus among concordant couples in at least two of the countries included wealth, spousal age difference, education, and both partners wanting another child. The discordant reports of recent sexual behavior and contraceptive use suggest that caution should be exercised when inferring couples' behavior from the report of one spouse, that concordant reports should be examined when possible, that methodological changes to improve the validity of spousal reports should be pursued, and that family planning and HIV-prevention programs should target those groups found to be using condoms and other contraceptives less frequently, particularly poorer couples.

  14. File list: ALL.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Neu.50.AllAg.Brain mm9 All antigens Neural Brain SRX661585,SRX218191,SRX188650,...,ERX513117,ERX370082,ERX370083,ERX370085,ERX370084,SRX150260,SRX150261 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/ALL.Neu.50.AllAg.Brain.bed ...

  15. File list: ALL.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  16. File list: ALL.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Neu.10.AllAg.Brain mm9 All antigens Neural Brain SRX661585,SRX188650,SRX191009,...,ERX339062,ERX339067,ERX513117,ERX370082,ERX370083,ERX370085,ERX370084 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/ALL.Neu.10.AllAg.Brain.bed ...

  17. File list: ALL.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Neu.20.AllAg.Brain mm9 All antigens Neural Brain SRX661585,SRX188650,SRX191009,...,SRX150260,SRX150261,ERX513117,ERX370082,ERX370083,ERX370085,ERX370084 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/ALL.Neu.20.AllAg.Brain.bed ...

  18. Report to users of ATLAS

    International Nuclear Information System (INIS)

    Ahmad, I.; Glagola, B.

    1997-03-01

    This report covers the following topics: (1) status of the ATLAS accelerator; (2) progress in R and D towards a proposal for a National ISOL Facility; (3) highlights of recent research at ATLAS; (4) the move of gammasphere from LBNL to ANL; (5) Accelerator Target Development laboratory; (6) Program Advisory Committee; (7) ATLAS User Group Executive Committee; and (8) ATLAS user handbook available in the World Wide Web. A brief summary is given for each topic

  19. Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

    Energy Technology Data Exchange (ETDEWEB)

    Bouchami, J; Dallaire, F; Gutierrez, A; Idarraga, J; Leroy, C; Picard, S; Scallon, O [Universite de Montreal, Montreal, Quebec H3C 3J7 (Canada); Kral, V; PospIsil, S; Solc, J; Suk, M; Turecek, D; Vykydal, Z; Zemlieka, J, E-mail: scallon@lps.umontreal.ca [Institute of Experimental and Applied Physics of the CTU in Prague, Horska 3a/22, CZ-12800 Praha2 - Albertov (Czech Republic)

    2011-01-15

    The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of {sup 6}LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) - based on the ROOT application - allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons ({sup 252}Cf and {sup 241}AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

  20. Estimate of the neutron fields in ATLAS based on ATLAS-MPX detectors data

    Science.gov (United States)

    Bouchami, J.; Dallaire, F.; Gutiérrez, A.; Idarraga, J.; Král, V.; Leroy, C.; Picard, S.; Pospíšil, S.; Scallon, O.; Solc, J.; Suk, M.; Turecek, D.; Vykydal, Z.; Žemlièka, J.

    2011-01-01

    The ATLAS-MPX detectors are based on Medipix2 silicon devices designed by CERN for the detection of different types of radiation. These detectors are covered with converting layers of 6LiF and polyethylene (PE) to increase their sensitivity to thermal and fast neutrons, respectively. These devices allow the measurement of the composition and spectroscopic characteristics of the radiation field in ATLAS, particularly of neutrons. These detectors can operate in low or high preset energy threshold mode. The signature of particles interacting in a ATLAS-MPX detector at low threshold are clusters of adjacent pixels with different size and form depending on their type, energy and incidence angle. The classification of particles into different categories can be done using the geometrical parameters of these clusters. The Medipix analysis framework (MAFalda) — based on the ROOT application — allows the recognition of particle tracks left in ATLAS-MPX devices located at various positions in the ATLAS detector and cavern. The pattern recognition obtained from the application of MAFalda was configured to distinguish the response of neutrons from other radiation. The neutron response at low threshold is characterized by clusters of adjoining pixels (heavy tracks and heavy blobs) left by protons and heavy ions resulting from neutron interactions in the converting layers of the ATLAS-MPX devices. The neutron detection efficiency of ATLAS-MPX devices has been determined by the exposure of two detectors of reference to radionuclide sources of neutrons (252Cf and 241AmBe). With these results, an estimate of the neutrons fields produced at the devices locations during ATLAS operation was done.

  1. Non-negative Tensor Factorization with missing data for the modeling of gene expressions in the Human Brain

    DEFF Research Database (Denmark)

    Nielsen, Søren Føns Vind; Mørup, Morten

    2014-01-01

    Non-negative Tensor Factorization (NTF) has become a prominent tool for analyzing high dimensional multi-way structured data. In this paper we set out to analyze gene expression across brain regions in multiple subjects based on data from the Allen Human Brain Atlas [1] with more than 40 % data m...

  2. ATLAS Colouring Book

    CERN Multimedia

    Anthony, Katarina

    2016-01-01

    The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  3. File list: Unc.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Unc.Neu.20.AllAg.Brain mm9 Unclassified Neural Brain SRX218191,SRX1125792,SRX112579...3,SRX1125795,SRX1125794,SRX218193,SRX218192,SRX017294,SRX218195,SRX218194,SRX1125797,SRX1125796 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Unc.Neu.20.AllAg.Brain.bed ...

  4. File list: Unc.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Unc.Neu.10.AllAg.Brain mm9 Unclassified Neural Brain SRX218191,SRX1125792,SRX112579...3,SRX218193,SRX017294,SRX218195,SRX1125795,SRX1125794,SRX218192,SRX1125797,SRX1125796,SRX218194 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Unc.Neu.10.AllAg.Brain.bed ...

  5. File list: Unc.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Unc.Neu.05.AllAg.Brain mm9 Unclassified Neural Brain SRX1125793,SRX1125792,SRX21819...5,SRX218191,SRX218193,SRX218194,SRX017294,SRX1125795,SRX1125794,SRX1125796,SRX1125797,SRX218192 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Unc.Neu.05.AllAg.Brain.bed ...

  6. File list: Unc.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Unc.Neu.50.AllAg.Brain mm9 Unclassified Neural Brain SRX218191,SRX1125793,SRX112579...2,SRX218193,SRX218192,SRX017294,SRX1125795,SRX1125794,SRX218195,SRX218194,SRX1125796,SRX1125797 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/Unc.Neu.50.AllAg.Brain.bed ...

  7. SU-E-J-128: Two-Stage Atlas Selection in Multi-Atlas-Based Image Segmentation

    International Nuclear Information System (INIS)

    Zhao, T; Ruan, D

    2015-01-01

    Purpose: In the new era of big data, multi-atlas-based image segmentation is challenged by heterogeneous atlas quality and high computation burden from extensive atlas collection, demanding efficient identification of the most relevant atlases. This study aims to develop a two-stage atlas selection scheme to achieve computational economy with performance guarantee. Methods: We develop a low-cost fusion set selection scheme by introducing a preliminary selection to trim full atlas collection into an augmented subset, alleviating the need for extensive full-fledged registrations. More specifically, fusion set selection is performed in two successive steps: preliminary selection and refinement. An augmented subset is first roughly selected from the whole atlas collection with a simple registration scheme and the corresponding preliminary relevance metric; the augmented subset is further refined into the desired fusion set size, using full-fledged registration and the associated relevance metric. The main novelty of this work is the introduction of an inference model to relate the preliminary and refined relevance metrics, based on which the augmented subset size is rigorously derived to ensure the desired atlases survive the preliminary selection with high probability. Results: The performance and complexity of the proposed two-stage atlas selection method were assessed using a collection of 30 prostate MR images. It achieved comparable segmentation accuracy as the conventional one-stage method with full-fledged registration, but significantly reduced computation time to 1/3 (from 30.82 to 11.04 min per segmentation). Compared with alternative one-stage cost-saving approach, the proposed scheme yielded superior performance with mean and medium DSC of (0.83, 0.85) compared to (0.74, 0.78). Conclusion: This work has developed a model-guided two-stage atlas selection scheme to achieve significant cost reduction while guaranteeing high segmentation accuracy. The benefit

  8. Whole brain imaging with Serial Two-Photon Tomography

    Directory of Open Access Journals (Sweden)

    Stephen P Amato

    2016-03-01

    Full Text Available Imaging entire mouse brains at submicron resolution has historically been a challenging undertaking and largely confined to the province of dedicated atlasing initiatives. The has limited systematic investigations into important areas of neuroscience, such as neural circuits, brain mapping and neurodegeneration. In this paper, we describe in detail Serial Two-Photon (STP tomography, a robust, reliable method for imaging entire brains with histological detail. We provide examples of how the basic methodology can be extended to other imaging modalities, such as optical coherence tomography, in order to provide unique contrast mechanisms. Furthermore we provide a survey of the research that STP tomography has enabled in the field of neuroscience, provide examples of how this technology enables quantitative whole brain studies, and discuss the current limitations of STP tomography-based approaches

  9. ATLAS Cloud R&D

    CERN Document Server

    Panitkin, S; The ATLAS collaboration; Caballero Bejar, J; Benjamin, D; DiGirolamo, A; Gable, I; Hendrix, V; Hover, J; Kucharczuk, K; Medrano LLamas, R; Love, P; Ohman, H; Paterson, M; Sobie, R; Taylor, R; Walker, R; Zaytsev, A

    2014-01-01

    The computing model of the ATLAS experiment was designed around the concept of grid computing and, since the start of data taking, this model has proven very successful. However, new cloud computing technologies bring attractive features to improve the operations and elasticity of scientific distributed computing. ATLAS sees grid and cloud computing as complementary technologies that will coexist at different levels of resource abstraction, and two years ago created an R&D working group to investigate the different integration scenarios. The ATLAS Cloud Computing R&D has been able to demonstrate the feasibility of offloading work from grid to cloud sites and, as of today, is able to integrate transparently various cloud resources into the PanDA workload management system. The ATLAS Cloud Computing R&D is operating various PanDA queues on private and public resources and has provided several hundred thousand CPU days to the experiment. As a result, the ATLAS Cloud Computing R&D group has gained...

  10. ATLAS MPGD production status

    CERN Document Server

    Schioppa, Marco; The ATLAS collaboration

    2018-01-01

    Micromegas (MICRO MEsh GAseous Structure) chambers are Micro-Pattern Gaseous Detectors designed to provide a high spatial resolution and reasonable good time resolution in highly irradiated environments. In 2007 an ambitious long-term R\\&D activity was started in the context of the ATLAS experiment, at CERN: the Muon ATLAS Micromegas Activity (MAMMA). After years of tests on prototypes and technology breakthroughs, Micromegas chambers were chosen as tracking detectors for an upgrade of the ATLAS Muon Spectrometer. These novel detectors will be installed in 2020 at the end of the second long shutdown of the Large Hadron Collider, and will serve mainly as precision detectors in the innermost part of the forward ATLAS Muon Spectrometer. Four different types of Micromegas modules, eight layers each, up to $3 m^2$ area (of unprecedented size), will cover a surface of $150 m^2$ for a total active area of about $1200 m^2$. With this upgrade the ATLAS muon system will maintain the full acceptance of its excellent...

  11. ATLAS' major cooling project

    CERN Multimedia

    2005-01-01

    In 2005, a considerable effort has been put into commissioning the various units of ATLAS' complex cryogenic system. This is in preparation for the imminent cooling of some of the largest components of the detector in their final underground configuration. The liquid helium and nitrogen ATLAS refrigerators in USA 15. Cryogenics plays a vital role in operating massive detectors such as ATLAS. In many ways the liquefied argon, nitrogen and helium are the life-blood of the detector. ATLAS could not function without cryogens that will be constantly pumped via proximity systems to the superconducting magnets and subdetectors. In recent weeks compressors at the surface and underground refrigerators, dewars, pumps, linkages and all manner of other components related to the cryogenic system have been tested and commissioned. Fifty metres underground The helium and nitrogen refrigerators, installed inside the service cavern, are an important part of the ATLAS cryogenic system. Two independent helium refrigerators ...

  12. ATLAS: Exceeding all expectations

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    “One year ago it would have been impossible for us to guess that the machine and the experiments could achieve so much so quickly”, says Fabiola Gianotti, ATLAS spokesperson. The whole chain – from collision to data analysis – has worked remarkably well in ATLAS.   The first LHC proton run undoubtedly exceeded expectations for the ATLAS experiment. “ATLAS has worked very well since the beginning. Its overall data-taking efficiency is greater than 90%”, says Fabiola Gianotti. “The quality and maturity of the reconstruction and simulation software turned out to be better than we expected for this initial stage of the experiment. The Grid is a great success, and right from the beginning it has allowed members of the collaboration all over the world to participate in the data analysis in an effective and timely manner, and to deliver physics results very quickly”. In just a few months of data taking, ATLAS has observed t...

  13. Future ATLAS Higgs Studies

    CERN Document Server

    Smart, Ben; The ATLAS collaboration

    2017-01-01

    The High-Luminosity LHC will prove a challenging environment to work in, with for example $=200$ expected. It will however also provide great opportunities for advancing studies of the Higgs boson. The ATLAS detector will be upgraded, and Higgs prospects analyses have been performed to assess the reach of ATLAS Higgs studies in the HL-LHC era. These analyses are presented, as are Run-2 ATLAS di-Higgs analyses for comparison.

  14. Concorde noise-induced building vibrations: International Airport Dulles. [studies by Langley Research Center

    Science.gov (United States)

    Mayes, W. H.; Scholl, H. F.; Stephens, D. G.; Holliday, B. G.; Deloach, R.; Finley, T. D.; Holmes, H. K.; Lewis, R. B.; Lynch, J. W.

    1977-01-01

    A series of studies were conducted to assess the noise-induced building vibrations associated with Concorde operations. The vibration levels of windows, walls, and floors were measured along with the associated noise levels of Concorde, subsonic aircraft and some nonaircraft events. Test sites included Sully Plantation which is adjacent to Dulles International Airport and three residential homes located in Montgomery County, Maryland. The measured vibration response levels due to Concorde operations were found to be: (1) higher than the levels due to other aircraft, (2) less than the levels due to certain household events which involve direct impulsive loading such as door and window closing, (3) less than criteria levels for building damage, and (4) comparable to levels which are perceptible to people.

  15. Concordance of autoimmune disease in a nationwide Danish systemic lupus erythematosus twin cohort

    DEFF Research Database (Denmark)

    Ulff-Møller, Constance Jensina; Svendsen, Anders Jørgen; Viemose, Louise Nørgaard

    2018-01-01

    OBJECTIVE: To determine the concordance of systemic lupus erythematosus (SLE) and co-aggregating autoimmune diseases among Danish twins. METHODS: SLE-affected twins were ascertained by record linkage between the National Patient Register (NPR) and the Danish Twin Registry (DTR). Registered SLE....... Another four co-twins had other autoimmune disease, corresponding to a probandwise concordance of any autoimmune disease of 50.0% in MZ (95% CI: 21.5-78.5) and 23.1% in DZ twins (95% CI: 8.18-50.3). CONCLUSION: Population-based Danish data suggest that SLE twin concordance is lower than previously...... reported, but still point to the importance of both genetic and environmental factors, and indicate a substantial co-aggregation of other autoimmune diseases in SLE twins....

  16. Fine-mapping the effects of Alzheimer's disease risk loci on brain morphology.

    Science.gov (United States)

    Roshchupkin, Gennady V; Adams, Hieab H; van der Lee, Sven J; Vernooij, Meike W; van Duijn, Cornelia M; Uitterlinden, Andre G; van der Lugt, Aad; Hofman, Albert; Niessen, Wiro J; Ikram, Mohammad A

    2016-12-01

    The neural substrate of genetic risk variants for Alzheimer's disease (AD) remains unknown. We studied their effect on healthy brain morphology to provide insight into disease etiology in the preclinical phase. We included 4071 nondemented, elderly participants of the population-based Rotterdam Study who underwent brain magnetic resonance imaging and genotyping. We performed voxel-based morphometry (VBM) on all gray-matter voxels for 19 previously identified, common AD risk variants. Whole-brain expression data from the Allen Human Brain Atlas was used to examine spatial overlap between VBM association results and expression of genes in AD risk loci regions. Brain regions most significantly associated with AD risk variants were the left postcentral gyrus with ABCA7 (rs4147929, p = 4.45 × 10 -6 ), right superior frontal gyrus by ZCWPW1 (rs1476679, p = 5.12 × 10 -6 ), and right postcentral gyrus by APOE (p = 6.91 × 10 -6 ). Although no individual voxel passed multiple-testing correction, we found significant spatial overlap between the effects of AD risk loci on VBM and the expression of genes (MEF2C, CLU, and SLC24A4) in the Allen Brain Atlas. Results are available online on www.imagene.nl/ADSNPs/. In this single largest imaging genetics data set worldwide, we found that AD risk loci affect cortical gray matter in several brain regions known to be involved in AD, as well as regions that have not been implicated before. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Organs at risk in the brain and their dose-constraints in adults and in children: A radiation oncologist’s guide for delineation in everyday practice

    International Nuclear Information System (INIS)

    Scoccianti, Silvia; Detti, Beatrice; Gadda, Davide; Greto, Daniela; Furfaro, Ilaria; Meacci, Fiammetta; Simontacchi, Gabriele; Di Brina, Lucia; Bonomo, Pierluigi; Giacomelli, Irene; Meattini, Icro; Mangoni, Monica; Cappelli, Sabrina; Cassani, Sara; Talamonti, Cinzia; Bordi, Lorenzo; Livi, Lorenzo

    2015-01-01

    Purpose: Accurate organs at risk definition is essential for radiation treatment of brain tumors. The aim of this study is to provide a stepwise and simplified contouring guide to delineate the OARs in the brain as it would be done in the everyday practice of planning radiotherapy for brain cancer treatment. Methods: Anatomical descriptions and neuroimaging atlases of the brain were studied. The dosimetric constraints used in literature were reviewed. Results: A Computed Tomography and Magnetic Resonance Imaging based detailed atlas was developed jointly by radiation oncologists, a neuroradiologist and a neurosurgeon. For each organ brief anatomical notion, main radiological reference points and useful considerations are provided. Recommended dose-constraints both for adult and pediatric patients were also provided. Conclusions: This report provides guidelines for OARs delineation and their dose-constraints for the treatment planning of patients with brain tumors

  18. Modeling Concordance Correlation Coefficient for Longitudinal Study Data

    Science.gov (United States)

    Ma, Yan; Tang, Wan; Yu, Qin; Tu, X. M.

    2010-01-01

    Measures of agreement are used in a wide range of behavioral, biomedical, psychosocial, and health-care related research to assess reliability of diagnostic test, psychometric properties of instrument, fidelity of psychosocial intervention, and accuracy of proxy outcome. The concordance correlation coefficient (CCC) is a popular measure of…

  19. Glance Information System for ATLAS Management

    International Nuclear Information System (INIS)

    Grael, F F; Maidantchik, C; Évora, L H R A; Karam, K; Moraes, L O F; Cirilli, M; Nessi, M; Pommès, K

    2011-01-01

    ATLAS Experiment is an international collaboration where more than 37 countries, 172 institutes and laboratories, 2900 physicists, engineers, and computer scientists plus 700 students participate. The management of this teamwork involves several aspects such as institute contribution, employment records, members' appointment, authors' list, preparation and publication of papers and speakers nomination. Previously, most of the information was accessible by a limited group and developers had to face problems such as different terminology, diverse data modeling, heterogeneous databases and unlike users needs. Moreover, the systems were not designed to handle new requirements. The maintenance has to be an easy task due to the long lifetime experiment and professionals turnover. The Glance system, a generic mechanism for accessing any database, acts as an intermediate layer isolating the user from the particularities of each database. It retrieves, inserts and updates the database independently of its technology and modeling. Relying on Glance, a group of systems were built to support the ATLAS management and operation aspects: ATLAS Membership, ATLAS Appointments, ATLAS Speakers, ATLAS Analysis Follow-Up, ATLAS Conference Notes, ATLAS Thesis, ATLAS Traceability and DSS Alarms Viewer. This paper presents the overview of the Glance information framework and describes the privilege mechanism developed to grant different level of access for each member and system.

  20. Glance Information System for ATLAS Management

    Science.gov (United States)

    Grael, F. F.; Maidantchik, C.; Évora, L. H. R. A.; Karam, K.; Moraes, L. O. F.; Cirilli, M.; Nessi, M.; Pommès, K.; ATLAS Collaboration

    2011-12-01

    ATLAS Experiment is an international collaboration where more than 37 countries, 172 institutes and laboratories, 2900 physicists, engineers, and computer scientists plus 700 students participate. The management of this teamwork involves several aspects such as institute contribution, employment records, members' appointment, authors' list, preparation and publication of papers and speakers nomination. Previously, most of the information was accessible by a limited group and developers had to face problems such as different terminology, diverse data modeling, heterogeneous databases and unlike users needs. Moreover, the systems were not designed to handle new requirements. The maintenance has to be an easy task due to the long lifetime experiment and professionals turnover. The Glance system, a generic mechanism for accessing any database, acts as an intermediate layer isolating the user from the particularities of each database. It retrieves, inserts and updates the database independently of its technology and modeling. Relying on Glance, a group of systems were built to support the ATLAS management and operation aspects: ATLAS Membership, ATLAS Appointments, ATLAS Speakers, ATLAS Analysis Follow-Up, ATLAS Conference Notes, ATLAS Thesis, ATLAS Traceability and DSS Alarms Viewer. This paper presents the overview of the Glance information framework and describes the privilege mechanism developed to grant different level of access for each member and system.

  1. ATLAS Cloud R&D

    Science.gov (United States)

    Panitkin, Sergey; Barreiro Megino, Fernando; Caballero Bejar, Jose; Benjamin, Doug; Di Girolamo, Alessandro; Gable, Ian; Hendrix, Val; Hover, John; Kucharczyk, Katarzyna; Medrano Llamas, Ramon; Love, Peter; Ohman, Henrik; Paterson, Michael; Sobie, Randall; Taylor, Ryan; Walker, Rodney; Zaytsev, Alexander; Atlas Collaboration

    2014-06-01

    The computing model of the ATLAS experiment was designed around the concept of grid computing and, since the start of data taking, this model has proven very successful. However, new cloud computing technologies bring attractive features to improve the operations and elasticity of scientific distributed computing. ATLAS sees grid and cloud computing as complementary technologies that will coexist at different levels of resource abstraction, and two years ago created an R&D working group to investigate the different integration scenarios. The ATLAS Cloud Computing R&D has been able to demonstrate the feasibility of offloading work from grid to cloud sites and, as of today, is able to integrate transparently various cloud resources into the PanDA workload management system. The ATLAS Cloud Computing R&D is operating various PanDA queues on private and public resources and has provided several hundred thousand CPU days to the experiment. As a result, the ATLAS Cloud Computing R&D group has gained a significant insight into the cloud computing landscape and has identified points that still need to be addressed in order to fully utilize this technology. This contribution will explain the cloud integration models that are being evaluated and will discuss ATLAS' learning during the collaboration with leading commercial and academic cloud providers.

  2. The Irish Wind Atlas

    Energy Technology Data Exchange (ETDEWEB)

    Watson, R [Univ. College Dublin, Dept. of Electronic and Electrical Engineering, Dublin (Ireland); Landberg, L [Risoe National Lab., Meteorology and Wind Energy Dept., Roskilde (Denmark)

    1999-03-01

    The development work on the Irish Wind Atlas is nearing completion. The Irish Wind Atlas is an updated improved version of the Irish section of the European Wind Atlas. A map of the irish wind resource based on a WA{sup s}P analysis of the measured data and station description of 27 measuring stations is presented. The results of previously presented WA{sup s}P/KAMM runs show good agreement with these results. (au)

  3. O Livro de Colorir da Experiência ATLAS - ATLAS Experiment Colouring Book in Portuguese

    CERN Multimedia

    Anthony, Katarina

    2017-01-01

    Language: Portuguese - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration. Língua: Português - O Livro de Colorir da Experiência ATLAS é um livro educacional gratuito para descarregar, ideal para crianças dos 5 aos 9 anos de idade. Este livro procura introduzir as crianças ao estudo da Física de Alta-Energia, bem como ao trabalho desenvolvido pela Colaboração ATLAS.

  4. Maľovanka Experiment ATLAS - ATLAS Experiment Colouring Book in Slovak

    CERN Multimedia

    Anthony, Katarina

    2017-01-01

    Language: Slovak - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  5. ATLAS Deneyi Boyama Kitabı - ATLAS Experiment Colouring Book in Turkish

    CERN Multimedia

    Anthony, Katarina

    2018-01-01

    Language: Turkish - The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  6. AGIS: The ATLAS Grid Information System

    Science.gov (United States)

    Anisenkov, A.; Di Girolamo, A.; Klimentov, A.; Oleynik, D.; Petrosyan, A.; Atlas Collaboration

    2014-06-01

    ATLAS, a particle physics experiment at the Large Hadron Collider at CERN, produced petabytes of data annually through simulation production and tens of petabytes of data per year from the detector itself. The ATLAS computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we describe the ATLAS Grid Information System (AGIS), designed to integrate configuration and status information about resources, services and topology of the computing infrastructure used by the ATLAS Distributed Computing applications and services.

  7. High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas.

    Science.gov (United States)

    Saygin, Z M; Kliemann, D; Iglesias, J E; van der Kouwe, A J W; Boyd, E; Reuter, M; Stevens, A; Van Leemput, K; McKee, A; Frosch, M P; Fischl, B; Augustinack, J C

    2017-07-15

    The amygdala is composed of multiple nuclei with unique functions and connections in the limbic system and to the rest of the brain. However, standard in vivo neuroimaging tools to automatically delineate the amygdala into its multiple nuclei are still rare. By scanning postmortem specimens at high resolution (100-150µm) at 7T field strength (n = 10), we were able to visualize and label nine amygdala nuclei (anterior amygdaloid, cortico-amygdaloid transition area; basal, lateral, accessory basal, central, cortical medial, paralaminar nuclei). We created an atlas from these labels using a recently developed atlas building algorithm based on Bayesian inference. This atlas, which will be released as part of FreeSurfer, can be used to automatically segment nine amygdala nuclei from a standard resolution structural MR image. We applied this atlas to two publicly available datasets (ADNI and ABIDE) with standard resolution T1 data, used individual volumetric data of the amygdala nuclei as the measure and found that our atlas i) discriminates between Alzheimer's disease participants and age-matched control participants with 84% accuracy (AUC=0.915), and ii) discriminates between individuals with autism and age-, sex- and IQ-matched neurotypically developed control participants with 59.5% accuracy (AUC=0.59). For both datasets, the new ex vivo atlas significantly outperformed (all p amygdala derived from the segmentation in FreeSurfer 5.1 (ADNI: 75%, ABIDE: 54% accuracy), as well as classification based on whole amygdala volume (using the sum of all amygdala nuclei volumes; ADNI: 81%, ABIDE: 55% accuracy). This new atlas and the segmentation tools that utilize it will provide neuroimaging researchers with the ability to explore the function and connectivity of the human amygdala nuclei with unprecedented detail in healthy adults as well as those with neurodevelopmental and neurodegenerative disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Evaluation of atlas-based autosegmentation with ABAS software for head-and-neck cancer

    International Nuclear Information System (INIS)

    Zhang Xiuchun; Hu Cairong; Chen Chuanben; Cai Yongjun

    2011-01-01

    Objective: To evaluate the autocontouring accuracy using the atlas-based autosegmentation of CT images for head-and-neck cancer. Methods: Ten head and neck patients with contours were selected. Two groups of autocontouring atlas were tested, the first group was for patients with own atlas, for the second group we tested the autocontouring of eight patients with other two patients atlas. Dice similarity coefficient (DSC) and overlap index (OI) were introduced to evaluate the autocontours, and the discrepancy between the two groups was evaluated through paired t-test. Results: Both the DSC and OI of all the organs in the first group were >0.80, the result of mandible was the highest (>0.91), the DSC of the gross tumor volume (GTV) was the lowest (0.81), the OI of the GTV was 0.82, and the DSC and OI of the clinical target volume (node) were 0.82 and 0, 79, respectively. Only the risk organ was delineated in the second group, and spinal cord and brain stem were combined to analyze. All the DSC was about 0.70, and the DSC and OI of mandible were higher than the others, which was due to its bone anatomy. The accuracy in the second group was significantly lower than that of the first group (t =3.24 - 8.26, P =0.014 -0.000), except the right parotid (t=2.08, P=0.075). Conclusions: Automatic segmentation generates contours of sufficient accuracy for adaptive planning intensity-modulated radiotherapy (IMRT) to accommodate anatomic changes during treatment. For convention planning IMRT normal structure auto-contouring,it need to select more standard atlas in order to acquire a satisfied autocontours. (authors)

  9. Mapping fetal brain development in utero using magnetic resonance imaging: the Big Bang of brain mapping.

    Science.gov (United States)

    Studholme, Colin

    2011-08-15

    The development of tools to construct and investigate probabilistic maps of the adult human brain from magnetic resonance imaging (MRI) has led to advances in both basic neuroscience and clinical diagnosis. These tools are increasingly being applied to brain development in adolescence and childhood, and even to neonatal and premature neonatal imaging. Even earlier in development, parallel advances in clinical fetal MRI have led to its growing use as a tool in challenging medical conditions. This has motivated new engineering developments encompassing optimal fast MRI scans and techniques derived from computer vision, the combination of which allows full 3D imaging of the moving fetal brain in utero without sedation. These promise to provide a new and unprecedented window into early human brain growth. This article reviews the developments that have led us to this point, examines the current state of the art in the fields of fast fetal imaging and motion correction, and describes the tools to analyze dynamically changing fetal brain structure. New methods to deal with developmental tissue segmentation and the construction of spatiotemporal atlases are examined, together with techniques to map fetal brain growth patterns.

  10. Concordance between maternal recall of birth complications and data from obstetrical records.

    Science.gov (United States)

    Keenan, Kate; Hipwell, Alison; McAloon, Rose; Hoffmann, Amy; Mohanty, Arpita; Magee, Kelsey

    2017-02-01

    Prenatal complications are associated with poor outcomes in the offspring. Access to medical records is limited in the United States and investigators often rely on maternal report of prenatal complications. We tested concordance between maternal recall and birth records in a community-based sample of mothers participating in a longitudinal study in order to determine the accuracy of maternal recall of perinatal complications. Participants were 151 biological mothers, who were interviewed about gestational age at birth, birthweight, and the most commonly occurring birth complications: nuchal cord and meconium aspiration when the female child was on average 6years old, and for whom birth records were obtained. Concordance between reports was assessed using one-way random intra-class coefficients for continuous measures and kappa coefficients for dichotomous outcomes. Associations between maternal demographic and psychological factors and discrepancies also were tested. Concordance was excellent for continuously measured birthweight (ICC=0.85, pbirth record and absence according to maternal recall. Receipt of public assistance was associated with a decrease in discrepancy in report of nuchal cord. Concordance between maternal retrospective report and medical birth records varies across different types of perinatal events. There was little evidence that demographic or psychological factors increased the risk of discrepancies. Maternal recall based on continuous measures of perinatal factors may yield more valid data than dichotomous outcomes. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  11. Preparing a new book on ATLAS

    CERN Multimedia

    Claudia Marcelloni de Oliveira

    A book about the ATLAS project and the ATLAS collaboration is going to be published and available for sale in mid 2008. The book is intended to be a symbol of appreciation for all the people from ATLAS institutes, triggering fond memories through photos, interviews, short commentaries and anecdotes about the daily life and milestones encountered while designing, constructing and completing ATLAS. We would like to give you the opportunity to collaborate with this project in two different ways: Firstly, please send us the best anecdotes related to ATLAS that you remember. To submit anecdotes, send an email to Claudia.Marcelloni@cern.ch. Secondly, you are invited to participate in our PHOTO COMPETITION. Please send the best photos you have of ATLAS attached with a description, the location, and date taken. The categories are: Milestones in the process of designing and building the detector, People at work and Important gatherings. To submit photos you should go to the CDS page and select ATLAS Photo Competi...

  12. Concordance of patient and caregiver reports in evaluating quality of life in patients with malignant gliomas and an assessment of caregiver burden

    Science.gov (United States)

    Jacobs, Daniel I.; Kumthekar, Priya; Stell, Becky V.; Grimm, Sean A.; Rademaker, Alfred W.; Rice, Laurie; Chandler, James P.; Muro, Kenji; Marymont, MaryAnne; Helenowski, Irene B.; Wagner, Lynne I.; Raizer, Jeffrey J.

    2014-01-01

    Background Given the neurocognitive impairment experienced by many patients with malignant gliomas, caregiver reports can be critical in assessing the quality of life (QOL) of these patients. In this study, we explored whether assessment of patient QOL by the primary caregiver shows concordance with the patient's self-reported QOL, and we quantified the burden faced by caregivers. Methods QOL of 45 patients was evaluated by both the patient and primary caregiver on 3 or more separate occasions using the Functional Assessment of Cancer Therapy-Brain (FACT-Br) instrument, and concordance between the 2 reports was evaluated. Caregiver burden was measured using the Caregiver Quality of Life Index-Cancer (CQOL-C) instrument. Results Overall, good concordance was observed between the patient and caregiver FACT-Br reports (intraclass correlation coefficient = 0.74). Patient-reported FACT-Br scores were 4.75 (95% CI, 1.44–8.05) points higher than paired caregiver reports on the 200-point scale (P = .008); however, this difference did not achieve clinical significance. Caregiver burden, as measured by the CQOL-C, was significantly greater among caregivers in this study than those previously reported for caregivers of patients with lung, breast, or prostate cancer (P < .001). Conclusions Despite minor discrepancies in caregiver assessments of patient QOL relative to patient self-reports, our results suggest that the caregiver assessments can serve as adequate proxies for patient reports. Our results also illustrate the particularly heavy burden faced by caregivers of patients with malignant glioma. Further research into both of these areas is warranted. PMID:26034616

  13. Brain morphology imaging by 3D microscopy and fluorescent Nissl staining.

    Science.gov (United States)

    Lazutkin, A A; Komissarova, N V; Toptunov, D M; Anokhin, K V

    2013-07-01

    Modern optical methods (multiphoton and light-sheet fluorescent microscopy) allow 3D imaging of large specimens of the brain with cell resolution. It is therefore essential to refer the resultant 3D pictures of expression of transgene, protein, and other markers in the brain to the corresponding structures in the atlas. This implies counterstaining of specimens with morphological dyes. However, there are no methods for contrasting large samples of the brain without their preliminary slicing. We have developed a method for fluorescent Nissl staining of whole brain samples. 3D reconstructions of specimens of the hippocampus, olfactory bulbs, and cortex were created. The method can be used for morphological control and evaluation of the effects of various factors on the brain using 3D microscopy technique.

  14. A quality control study on cytotechnologist-cytopathologist concordance and its relationship to the number of dots on the slide.

    Science.gov (United States)

    Bongiovanni, Massimo; De Saussure, Barbara; Kumar, Neeta; Pache, Jean-Claude; Cibas, Edmund S

    2009-01-01

    To study cytotechnologist (CT)-cytopathologist (CP) concordance for evaluating individual CTs' performance and for quality assurance and educational feedback. The interpretations of individual CTs were compared with the final interpretations (according to the 2001 Bethesda System) of the CP. Concordance percentages and kappa values were calculated for each CT and correlated with the numbers of dots on each slide, years of experience and percentage of work hours devoted to cytology. A total of 10,453 Pap tests were screened by 9 CTs during one year, out of which 993 (9.5%) were referred to one CP for a final interpretation. Mean concordance between the aggregate CT interpretations and those of the CP was 65.5%. Five CTs had good concordance, 3 had moderately good concordance, and one had surprisingly poor concordance that contrasted with good subjective impressions. No correlation was found between concordance and the average number of dots per slide, screening experience in cervicovaginal cytology or percentage of work hours devoted to cytology. Monitoring CT-CP concordance rates can unveil performance issues not detected by subjective impressions. An excessive number of dots per slide may not reflect poor diagnostic precision so much as a lack of confidence in interpretation.

  15. ATLAS B-physics potential

    International Nuclear Information System (INIS)

    Smizanska, M.

    2001-01-01

    Studies since 1993 have demonstrated the ability of ATLAS to pursue a wide B physics program. This document presents the latest performance studies with special stress on lepton identification. B-decays containing several leptons in ATLAS statistically dominate the high-precision measurements. We present new results on physics simulations of CP violation measurements in the B s 0 → J/Ψphi decay and on a novel ATLAS programme on beauty production in central proton-proton collisions of LHC

  16. Impairment of interrelated iron- and copper homeostatic mechanisms in brain contributes to the pathogenesis of neurodegenerative disorders

    DEFF Research Database (Denmark)

    Skjørringe, Tina; Møller, Lisbeth Birk; Moos, Torben

    2012-01-01

    is strictly regulated, and concordantly protective barriers, i.e., the blood-brain barrier (BBB) and the blood-cerebrospinal fluid (CSF) barrier (BCB) have evolved to separate the brain environment from the circulation. The uptake mechanisms of the two metals interact. Both iron deficiency and overload lead...... involved in iron transport. Iron and copper are mainly taken up at the BBB, but the BCB also plays a vital role in the homeostasis of the two metals, in terms of sequestering, uptake, and efflux of iron and copper from the brain. Inside the brain, iron and copper are taken up by neurons and glia cells...

  17. Clustering of Whole-Brain White Matter Short Association Bundles Using HARDI Data

    Directory of Open Access Journals (Sweden)

    Claudio Román

    2017-12-01

    Full Text Available Human brain connectivity is extremely complex and variable across subjects. While long association and projection bundles are stable and have been deeply studied, short association bundles present higher intersubject variability, and few studies have been carried out to adequately describe the structure, shape, and reproducibility of these bundles. However, their analysis is crucial to understand brain function and better characterize the human connectome. In this study, we propose an automatic method to identify reproducible short association bundles of the superficial white matter, based on intersubject hierarchical clustering. The method is applied to the whole brain and finds representative clusters of similar fibers belonging to a group of subjects, according to a distance metric between fibers. We experimented with both affine and non-linear registrations and, due to better reproducibility, chose the results obtained from non-linear registration. Once the clusters are calculated, our method performs automatic labeling of the most stable connections based on individual cortical parcellations. We compare results between two independent groups of subjects from a HARDI database to generate reproducible connections for the creation of an atlas. To perform a better validation of the results, we used a bagging strategy that uses pairs of groups of 27 subjects from a database of 74 subjects. The result is an atlas with 44 bundles in the left hemisphere and 49 in the right hemisphere, of which 33 bundles are found in both hemispheres. Finally, we use the atlas to automatically segment 78 new subjects from a different HARDI database and to analyze stability and lateralization results.

  18. ATLAS Award for Shield Supplier

    CERN Multimedia

    2004-01-01

    ATLAS technical coordinator Dr. Marzio Nessi presents the ATLAS supplier award to Vojtech Novotny, Director General of Skoda Hute.On 3 November, the ATLAS experiment honoured one of its suppliers, Skoda Hute s.r.o., of Plzen, Czech Republic, for their work on the detector's forward shielding elements. These huge and very massive cylinders surround the beampipe at either end of the detector to block stray particles from interfering with the ATLAS's muon chambers. For the shields, Skoda Hute produced 10 cast iron pieces with a total weight of 780 tonnes at a cost of 1.4 million CHF. Although there are many iron foundries in the CERN member states, there are only a limited number that can produce castings of the necessary size: the large pieces range in weight from 59 to 89 tonnes and are up to 1.5 metres thick.The forward shielding was designed by the ATLAS Technical Coordination in close collaboration with the ATLAS groups from the Czech Technical University and Charles University in Prague. The Czech groups a...

  19. ATLAS Facility Description Report

    International Nuclear Information System (INIS)

    Kang, Kyoung Ho; Moon, Sang Ki; Park, Hyun Sik; Cho, Seok; Choi, Ki Yong

    2009-04-01

    A thermal-hydraulic integral effect test facility, ATLAS (Advanced Thermal-hydraulic Test Loop for Accident Simulation), has been constructed at KAERI (Korea Atomic Energy Research Institute). The ATLAS has the same two-loop features as the APR1400 and is designed according to the well-known scaling method suggested by Ishii and Kataoka to simulate the various test scenarios as realistically as possible. It is a half-height and 1/288-volume scaled test facility with respect to the APR1400. The fluid system of the ATLAS consists of a primary system, a secondary system, a safety injection system, a break simulating system, a containment simulating system, and auxiliary systems. The primary system includes a reactor vessel, two hot legs, four cold legs, a pressurizer, four reactor coolant pumps, and two steam generators. The secondary system of the ATLAS is simplified to be of a circulating loop-type. Most of the safety injection features of the APR1400 and the OPR1000 are incorporated into the safety injection system of the ATLAS. In the ATLAS test facility, about 1300 instrumentations are installed to precisely investigate the thermal-hydraulic behavior in simulation of the various test scenarios. This report describes the scaling methodology, the geometric data of the individual component, and the specification and the location of the instrumentations in detail

  20. TU-CD-BRA-05: Atlas Selection for Multi-Atlas-Based Image Segmentation Using Surrogate Modeling

    International Nuclear Information System (INIS)

    Zhao, T; Ruan, D

    2015-01-01

    Purpose: The growing size and heterogeneity in training atlas necessitates sophisticated schemes to identify only the most relevant atlases for the specific multi-atlas-based image segmentation problem. This study aims to develop a model to infer the inaccessible oracle geometric relevance metric from surrogate image similarity metrics, and based on such model, provide guidance to atlas selection in multi-atlas-based image segmentation. Methods: We relate the oracle geometric relevance metric in label space to the surrogate metric in image space, by a monotonically non-decreasing function with additive random perturbations. Subsequently, a surrogate’s ability to prognosticate the oracle order for atlas subset selection is quantified probabilistically. Finally, important insights and guidance are provided for the design of fusion set size, balancing the competing demands to include the most relevant atlases and to exclude the most irrelevant ones. A systematic solution is derived based on an optimization framework. Model verification and performance assessment is performed based on clinical prostate MR images. Results: The proposed surrogate model was exemplified by a linear map with normally distributed perturbation, and verified with several commonly-used surrogates, including MSD, NCC and (N)MI. The derived behaviors of different surrogates in atlas selection and their corresponding performance in ultimate label estimate were validated. The performance of NCC and (N)MI was similarly superior to MSD, with a 10% higher atlas selection probability and a segmentation performance increase in DSC by 0.10 with the first and third quartiles of (0.83, 0.89), compared to (0.81, 0.89). The derived optimal fusion set size, valued at 7/8/8/7 for MSD/NCC/MI/NMI, agreed well with the appropriate range [4, 9] from empirical observation. Conclusion: This work has developed an efficacious probabilistic model to characterize the image-based surrogate metric on atlas selection

  1. Personal, family and social functioning among older couples concordant and discordant for high-risk alcohol consumption.

    Science.gov (United States)

    Moos, Rudolf H; Schutte, Kathleen K; Brennan, Penny L; Moos, Bernice S

    2011-02-01

    This study compares the personal, family and social functioning of older husbands and wives concordant or discordant for high-risk alcohol consumption and identifies predictors of changes in concordance and high-risk consumption. Three groups of couples were identified at baseline and followed 10 years later: (i) concordant couples in which husbands and wives engaged in low-risk alcohol consumption (n = 54); (ii) concordant couples in which husbands and wives engaged in high-risk alcohol consumption (n = 38); and (iii) discordant couples in which one partner engaged in high-risk alcohol consumption and the other partner did not (n = 75). At each follow-up, husbands and wives completed an inventory that assessed their personal, family and social functioning. Compared to the low-risk concordant group, husbands and wives in the high-risk concordant group were more likely to rely on tension-reduction coping, reported more friend approval of drinking, and were less involved in religious activities; however, they did not differ in the quality of the spousal relationship. The frequency of alcohol consumption declined among husbands in discordant couples, but not among husbands in concordant couples. Predictors of high-risk drinking included tension-reduction coping, friend approval of drinking and, for husbands, their wives' level of drinking. High-risk and discordant alcohol consumption do not seem to be linked to decrements in family functioning among older couples in long-term stable marriages. The predictors of heavy alcohol consumption among older husbands and wives identify points of intervention that may help to reduce their high-risk drinking. © 2010 Society for the Study of Addiction. No claim to US government works.

  2. Taking ATLAS to new heights

    CERN Document Server

    Abha Eli Phoboo, ATLAS experiment

    2013-01-01

    Earlier this month, 51 members of the ATLAS collaboration trekked up to the highest peak in the Atlas Mountains, Mt. Toubkal (4,167m), in North Africa.    The physicists were in Marrakech, Morocco, attending the ATLAS Overview Week (7 - 11 October), which was held for the first time on the African continent. Around 300 members of the collaboration met to discuss the status of the LS1 upgrades and plans for the next run of the LHC. Besides the trek, 42 ATLAS members explored the Saharan sand dunes of Morocco on camels.  Photos courtesy of Patrick Jussel.

  3. ATLAS DataFlow Infrastructure: Recent results from ATLAS cosmic and first-beam data-taking

    Energy Technology Data Exchange (ETDEWEB)

    Vandelli, Wainer, E-mail: wainer.vandelli@cern.c

    2010-04-01

    The ATLAS DataFlow infrastructure is responsible for the collection and conveyance of event data from the detector front-end electronics to the mass storage. Several optimized and multi-threaded applications fulfill this purpose operating over a multi-stage Gigabit Ethernet network which is the backbone of the ATLAS Trigger and Data Acquisition System. The system must be able to efficiently transport event-data with high reliability, while providing aggregated bandwidths larger than 5 GByte/s and coping with many thousands network connections. Nevertheless, routing and streaming capabilities and monitoring and data accounting functionalities are also fundamental requirements. During 2008, a few months of ATLAS cosmic data-taking and the first experience with the LHC beams provided an unprecedented test-bed for the evaluation of the performance of the ATLAS DataFlow, in terms of functionality, robustness and stability. Besides, operating the system far from its design specifications helped in exercising its flexibility and contributed in understanding its limitations. Moreover, the integration with the detector and the interfacing with the off-line data processing and management have been able to take advantage of this extended data taking-period as well. In this paper we report on the usage of the DataFlow infrastructure during the ATLAS data-taking. These results, backed-up by complementary performance tests, validate the architecture of the ATLAS DataFlow and prove that the system is robust, flexible and scalable enough to cope with the final requirements of the ATLAS experiment.

  4. ATLAS DataFlow Infrastructure: Recent results from ATLAS cosmic and first-beam data-taking

    International Nuclear Information System (INIS)

    Vandelli, Wainer

    2010-01-01

    The ATLAS DataFlow infrastructure is responsible for the collection and conveyance of event data from the detector front-end electronics to the mass storage. Several optimized and multi-threaded applications fulfill this purpose operating over a multi-stage Gigabit Ethernet network which is the backbone of the ATLAS Trigger and Data Acquisition System. The system must be able to efficiently transport event-data with high reliability, while providing aggregated bandwidths larger than 5 GByte/s and coping with many thousands network connections. Nevertheless, routing and streaming capabilities and monitoring and data accounting functionalities are also fundamental requirements. During 2008, a few months of ATLAS cosmic data-taking and the first experience with the LHC beams provided an unprecedented test-bed for the evaluation of the performance of the ATLAS DataFlow, in terms of functionality, robustness and stability. Besides, operating the system far from its design specifications helped in exercising its flexibility and contributed in understanding its limitations. Moreover, the integration with the detector and the interfacing with the off-line data processing and management have been able to take advantage of this extended data taking-period as well. In this paper we report on the usage of the DataFlow infrastructure during the ATLAS data-taking. These results, backed-up by complementary performance tests, validate the architecture of the ATLAS DataFlow and prove that the system is robust, flexible and scalable enough to cope with the final requirements of the ATLAS experiment.

  5. File list: His.Lar.50.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lar.50.AllAg.Larval_brain dm3 Histone Larvae Larval brain SRX1426943,SRX1426945... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/His.Lar.50.AllAg.Larval_brain.bed ...

  6. File list: His.Lar.10.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lar.10.AllAg.Larval_brain dm3 Histone Larvae Larval brain SRX1426945,SRX1426943... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/His.Lar.10.AllAg.Larval_brain.bed ...

  7. File list: His.Lar.20.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lar.20.AllAg.Larval_brain dm3 Histone Larvae Larval brain SRX1426943,SRX1426945... http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/His.Lar.20.AllAg.Larval_brain.bed ...

  8. Role of 18F-FDG PET/CT in primary brain lymphoma.

    Science.gov (United States)

    de-Bonilla-Damiá, Á; Fernández-López, R; Capote-Huelva, F J; de la Cruz-Vicente, F; Egea-Guerrero, J J; Borrego-Dorado, I

    To study the usefulness of 18 F-FDG PET/CT in the initial evaluation and in the response assessment in primary brain lymphoma. A retrospective analysis was carried out on 18 patients diagnosed with primary brain lymphoma, a histological subtype of diffuse large B-cell lymphoma, on whom an initial 18 F-FDG PET/CT and MRI was performed, with 7 of the cases being analysed after the completion of treatment in order to assess response and clinical follow up. Initial 18 F-FDG PET/CT showed 26 hypermetabolic foci, whereas 46 lesions were detected by MRI. The average SUV maximum of the lesions was 17.56 with T/N 3.55. The concordance of both tests for identifying the same number of lesions was moderate, obtaining a kappa index of 0.395 (P<.001). In the evaluation of treatment, MRI identified 16 lesions compared to 7 pathological accumulations observed by 18 F-FDG PET/CT. The concordance of both tests to assess type of response to treatment was moderate (kappa index 0.41) (P=.04). In both the initial evaluation and the assessment of the response to treatment, PET/CT led to a change strategy in 22% of patients who had lesions outside the cerebral parenchyma. MRI appears to be the method of choice for detecting brain disease in patients with primary brain lymphoma, whereas 18 F-FDG PET/CT seems to play a relevant role in the assessment of extra-cerebral disease. Copyright © 2017 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

  9. Prostatome: A combined anatomical and disease based MRI atlas of the prostate

    Energy Technology Data Exchange (ETDEWEB)

    Rusu, Mirabela; Madabhushi, Anant, E-mail: anant.madabhushi@case.edu [Case Western Reserve University, Cleveland, Ohio 44106 (United States); Bloch, B. Nicolas; Jaffe, Carl C. [Boston University School of Medicine, Boston, Massachusetts 02118 (United States); Genega, Elizabeth M. [Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215 (United States); Lenkinski, Robert E.; Rofsky, Neil M. [UT Southwestern Medical Center, Dallas, Texas 75235 (United States); Feleppa, Ernest [Riverside Research Institute, New York, New York 10038 (United States)

    2014-07-15

    Purpose: In this work, the authors introduce a novel framework, the anatomically constrained registration (AnCoR) scheme and apply it to create a fused anatomic-disease atlas of the prostate which the authors refer to as the prostatome. The prostatome combines a MRI based anatomic and a histology based disease atlas. Statistical imaging atlases allow for the integration of information across multiple scales and imaging modalities into a single canonical representation, in turn enabling a fused anatomical-disease representation which may facilitate the characterization of disease appearance relative to anatomic structures. While statistical atlases have been extensively developed and studied for the brain, approaches that have attempted to combine pathology and imaging data for study of prostate pathology are not extant. This works seeks to address this gap. Methods: The AnCoR framework optimizes a scoring function composed of two surface (prostate and central gland) misalignment measures and one intensity-based similarity term. This ensures the correct mapping of anatomic regions into the atlas, even when regional MRI intensities are inconsistent or highly variable between subjects. The framework allows for creation of an anatomic imaging and a disease atlas, while enabling their fusion into the anatomic imaging-disease atlas. The atlas presented here was constructed using 83 subjects with biopsy confirmed cancer who had pre-operative MRI (collected at two institutions) followed by radical prostatectomy. The imaging atlas results from mapping thein vivo MRI into the canonical space, while the anatomic regions serve as domain constraints. Elastic co-registration MRI and corresponding ex vivo histology provides “ground truth” mapping of cancer extent on in vivo imaging for 23 subjects. Results: AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework

  10. Prostatome: A combined anatomical and disease based MRI atlas of the prostate

    International Nuclear Information System (INIS)

    Rusu, Mirabela; Madabhushi, Anant; Bloch, B. Nicolas; Jaffe, Carl C.; Genega, Elizabeth M.; Lenkinski, Robert E.; Rofsky, Neil M.; Feleppa, Ernest

    2014-01-01

    Purpose: In this work, the authors introduce a novel framework, the anatomically constrained registration (AnCoR) scheme and apply it to create a fused anatomic-disease atlas of the prostate which the authors refer to as the prostatome. The prostatome combines a MRI based anatomic and a histology based disease atlas. Statistical imaging atlases allow for the integration of information across multiple scales and imaging modalities into a single canonical representation, in turn enabling a fused anatomical-disease representation which may facilitate the characterization of disease appearance relative to anatomic structures. While statistical atlases have been extensively developed and studied for the brain, approaches that have attempted to combine pathology and imaging data for study of prostate pathology are not extant. This works seeks to address this gap. Methods: The AnCoR framework optimizes a scoring function composed of two surface (prostate and central gland) misalignment measures and one intensity-based similarity term. This ensures the correct mapping of anatomic regions into the atlas, even when regional MRI intensities are inconsistent or highly variable between subjects. The framework allows for creation of an anatomic imaging and a disease atlas, while enabling their fusion into the anatomic imaging-disease atlas. The atlas presented here was constructed using 83 subjects with biopsy confirmed cancer who had pre-operative MRI (collected at two institutions) followed by radical prostatectomy. The imaging atlas results from mapping thein vivo MRI into the canonical space, while the anatomic regions serve as domain constraints. Elastic co-registration MRI and corresponding ex vivo histology provides “ground truth” mapping of cancer extent on in vivo imaging for 23 subjects. Results: AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework

  11. Brief retrospection on Hungarian school atlases

    Science.gov (United States)

    Klinghammer, István; Jesús Reyes Nuñez, José

    2018-05-01

    The first part of this article is dedicated to the history of Hungarian school atlases to the end of the 1st World War. Although the first maps included in a Hungarian textbook were probably made in 1751, the publication of atlases for schools is dated almost 50 years later, when professor Ézsáiás Budai created his "New School Atlas for elementary pupils" in 1800. This was followed by a long period of 90 years, when the school atlases were mostly translations and adaptations of foreign atlases, the majority of which were made in German-speaking countries. In those years, a school atlas made by a Hungarian astronomer, Antal Vállas, should be highlighted as a prominent independent piece of work. In 1890, a talented cartographer, Manó Kogutowicz founded the Hungarian Geographical Institute, which was the institution responsible for producing school atlases for the different types of schools in Hungary. The professional quality of the school atlases published by his institute was also recognized beyond the Hungarian borders by prizes won in international exhibitions. Kogutowicz laid the foundations of the current Hungarian school cartography: this statement is confirmed in the second part of this article, when three of his school atlases are presented in more detail to give examples of how the pupils were introduced to the basic cartographic and astronomic concepts as well as how different innovative solutions were used on the maps.

  12. The concordance between self-reported medication use and pharmacy records in pregnant women.

    Science.gov (United States)

    Cheung, K; El Marroun, H; Elfrink, M E; Jaddoe, V W V; Visser, L E; Stricker, B H Ch

    2017-09-01

    Several studies have been conducted to assess determinants affecting the performance or accuracy of self-reports. These studies are often not focused on pregnant women, or medical records were used as a data source where it is unclear if medications have been dispensed. Therefore, our objective was to evaluate the concordance between self-reported medication data and pharmacy records among pregnant women and its determinants. We conducted a population-based cohort study within the Generation R study, in 2637 pregnant women. The concordance between self-reported medication data and pharmacy records was calculated for different therapeutic classes using Yule's Y. We evaluated a number of variables as determinant of discordance between both sources through univariate and multivariate logistic regression analysis. The concordance between self-reports and pharmacy records was moderate to good for medications used for chronic conditions, such as selective serotonin reuptake inhibitors or anti-asthmatic medications (0.88 and 0.68, respectively). Medications that are used occasionally, such as antibiotics, had a lower concordance (0.51). Women with a Turkish or other non-Western background were more likely to demonstrate discordance between pharmacy records and self-reported data compared with women with a Dutch background (Turkish: odds ratio, 1.63; 95% confidence interval, 1.16-2.29; other non-Western: odds ratio, 1.33; 95% confidence interval, 1.03-1.71). Further research is needed to assess how the cultural or ethnic differences may affect the concordance or discordance between both medication sources. The results of this study showed that the use of multiple sources is needed to have a good estimation of the medication use during pregnancy. Copyright © 2017 John Wiley & Sons, Ltd.

  13. File list: DNS.Neu.05.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available DNS.Neu.05.AllAg.Adult_brains hg19 DNase-seq Neural Adult brains SRX189408,SRX18941...3 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/DNS.Neu.05.AllAg.Adult_brains.bed ...

  14. File list: DNS.Neu.10.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  15. File list: ALL.Neu.50.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  16. File list: DNS.Neu.50.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  17. File list: DNS.Neu.20.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available DNS.Neu.20.AllAg.Adult_brains hg19 DNase-seq Neural Adult brains SRX189408,SRX18941...3 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/DNS.Neu.20.AllAg.Adult_brains.bed ...

  18. File list: ALL.Neu.05.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. File list: ALL.Neu.20.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Neu.20.AllAg.Fetal_brain hg19 All antigens Neural Fetal brain SRX142786,SRX2096...60882 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/ALL.Neu.20.AllAg.Fetal_brain.bed ...

  20. Concordance among remission and admission diagnoses at intensive care unit, Hospital Universitario San José, Popayán, 2011

    Directory of Open Access Journals (Sweden)

    Victor Daniel Montenegro

    2012-03-01

    Full Text Available There are few published studies about diagnostic concordance in hospital services. The objective of this study was to calculate the concordance among remission and admission diagnoses from Hospital Universitario San José adult intensive care unit (I.C.U. of Popayán, 2011. Methods: Descriptive and retrospective study about concordance between the main remission and admission diagnoses from patients admitted in the Hospital adult intensive care unit; 914 patients were studied from the intensive care unit database, months January to December 2011. Statistical analysis about sociodemographic variables was performed, and Kappa index according to Landis and Koch scale among remission and admission diagnoses defined as priority was calculated. Results: It was found al almost perfect level of concordance in the diagnoses pancreatitis and intoxication, a substantial level of concordance in the diagnoses acute coronary syndrome, convulsive status, gastric cancer and eclampsia, a moderate level of concordance in the diagnoses stroke, head trauma, politraumatism and cardiac failure, and a fair level of concordance in the diagnoses sepsis, pneumonia, chronic obstructive pulmonary disease (COPD, gastrointestinal bleeding, acute respiratory infection and acute respiratory distress syndrome. Conclusion: Six of the seventeen studied diagnoses presented an outstanding concordance level; this can be related to factors such as: physicians’, diagnostic ability, provenance of the patients remitted to the I.C.U. and diagnostic coding made by health staff.

  1. Can Confirmation Measures Reflect Statistically Sound Dependencies in Data? The Concordance-based Assessment

    Directory of Open Access Journals (Sweden)

    Susmaga Robert

    2018-03-01

    Full Text Available The paper considers particular interestingness measures, called confirmation measures (also known as Bayesian confirmation measures, used for the evaluation of “if evidence, then hypothesis” rules. The agreement of such measures with a statistically sound (significant dependency between the evidence and the hypothesis in data is thoroughly investigated. The popular confirmation measures were not defined to possess such form of agreement. However, in error-prone environments, potential lack of agreement may lead to undesired effects, e.g. when a measure indicates either strong confirmation or strong disconfirmation, while in fact there is only weak dependency between the evidence and the hypothesis. In order to detect and prevent such situations, the paper employs a coefficient allowing to assess the level of dependency between the evidence and the hypothesis in data, and introduces a method of quantifying the level of agreement (referred to as a concordance between this coefficient and the measure being analysed. The concordance is characterized and visualised using specialized histograms, scatter-plots, etc. Moreover, risk-related interpretations of the concordance are introduced. Using a set of 12 confirmation measures, the paper presents experiments designed to establish the actual concordance as well as other useful characteristics of the measures.

  2. File list: ALL.Neu.50.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Neu.50.AllAg.Adult_brains hg19 All antigens Neural Adult brains SRX643470,SRX11...189408,SRX189413 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/ALL.Neu.50.AllAg.Adult_brains.bed ...

  3. File list: ALL.Neu.10.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: ALL.Neu.20.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: DNS.Neu.50.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  6. File list: DNS.Neu.20.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  7. File list: ALL.Neu.05.AllAg.Adult_brains [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Neu.05.AllAg.Adult_brains hg19 All antigens Neural Adult brains SRX643470,SRX01...189408,SRX189413 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/ALL.Neu.05.AllAg.Adult_brains.bed ...

  8. File list: DNS.Neu.10.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available DNS.Neu.10.AllAg.Fetal_brain hg19 DNase-seq Neural Fetal brain SRX040380,SRX040395,...6,SRX121278 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/DNS.Neu.10.AllAg.Fetal_brain.bed ...

  9. ATLAS Maintenance and Operation management system

    CERN Document Server

    Copy, B

    2007-01-01

    The maintenance and operation of the ATLAS detector will involve thousands of contributors from 170 physics institutes. Planning and coordinating the action of ATLAS members, ensuring their expertise is properly leveraged and that no parts of the detector are understaffed or overstaffed will be a challenging task. The ATLAS Maintenance and Operation application (referred to as Operation Task Planner inside the ATLAS experiment) offers a fluent web based interface that combines the flexibility and comfort of a desktop application, intuitive data visualization and navigation techniques, with a lightweight service oriented architecture. We will review the application, its usage within the ATLAS experiment, its underlying design and implementation.

  10. Concordance of mother-daughter diurnal cortisol production: Understanding the intergenerational transmission of risk for depression.

    Science.gov (United States)

    LeMoult, Joelle; Chen, Michael C; Foland-Ross, Lara C; Burley, Hannah W; Gotlib, Ian H

    2015-05-01

    A growing body of research is demonstrating concordance between mother and child diurnal cortisol production. In the context of maternal history of depression, intergenerational concordance of cortisol production could contribute to hypercortisolemia in children of depressed mothers, which has been shown to increase risk for MDD. The current study is the first to examine concordance in diurnal cortisol production between mothers with a history of depression and their never-depressed, but high-risk, children. We collected salivary cortisol across 2 days from mothers with (remitted; RMD) and without (CTL) a history of recurrent episodes of depression and their never-depressed daughters. As expected, RMD mothers and their daughters both exhibited higher cortisol production than did their CTL counterparts. Moreover, both across and within groups, mothers' and daughters' cortisol production were directly coupled. These findings suggest that there is an intergenerational concordance in cortisol dysregulation that may contribute to hypercortisolemia in girls at familial risk for depression. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Taus at ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Demers, Sarah M. [Yale Univ., New Haven, CT (United States). Dept. of Physics

    2017-12-06

    The grant "Taus at ATLAS" supported the group of Sarah Demers at Yale University over a period of 8.5 months, bridging the time between her Early Career Award and her inclusion on Yale's grant cycle within the Department of Energy's Office of Science. The work supported the functioning of the ATLAS Experiment at CERN's Large Hadron Collider and the analysis of ATLAS data. The work included searching for the Higgs Boson in a particular mode of its production (with a W or Z boson) and decay (to a pair of tau leptons.) This was part of a broad program of characterizing the Higgs boson as we try to understand this recently discovered particle, and whether or not it matches our expectations within the current standard model of particle physics. In addition, group members worked with simulation to understand the physics reach of planned upgrades to the ATLAS experiment. Supported group members include postdoctoral researcher Lotte Thomsen and graduate student Mariel Pettee.

  12. Soft QCD at CMS and ATLAS

    CERN Document Server

    Starovoitov, Pavel; The ATLAS collaboration

    2018-01-01

    A short overview of the recent soft QCD results from the ATLAS and CMS collaborations is presented. The inelastic cross section measurement by CMS at 13 TeV is summarised. The contribution of the diffractive processes to the very forward photon spectra studied by ATLAS and LHCf is discussed. The ATLAS measurements of the exclusive two-photon production of the muon pairs is presented and compared to the previous ATLAS and CMS results.

  13. AGIS: The ATLAS Grid Information System

    OpenAIRE

    Anisenkov, Alexey; Belov, Sergey; Di Girolamo, Alessandro; Gayazov, Stavro; Klimentov, Alexei; Oleynik, Danila; Senchenko, Alexander

    2012-01-01

    ATLAS is a particle physics experiment at the Large Hadron Collider at CERN. The experiment produces petabytes of data annually through simulation production and tens petabytes of data per year from the detector itself. The ATLAS Computing model embraces the Grid paradigm and a high degree of decentralization and computing resources able to meet ATLAS requirements of petabytes scale data operations. In this paper we present ATLAS Grid Information System (AGIS) designed to integrate configurat...

  14. ATLAS B-physics potential

    CERN Document Server

    Smizanska, M

    2001-01-01

    Studies since 1993 have demonstrated the ability of ATLAS to pursue a wide B physics program. This document presents the latest performance studies with special stress on lepton identification. B-decays containing several leptons in ATLAS statistically dominate the high- precision measurements. We present new results on physics simulations of CP violation measurements in the B/sub s//sup 0/ to J/ psi phi decay and on a novel ATLAS programme on beauty production in central proton-proton collisions at the LHC. (7 refs).

  15. Price squeezes in electric power: The new Battle of Concord

    International Nuclear Information System (INIS)

    Kwoka, J.E. Jr.

    1992-01-01

    The US Court of Appeals opinion in Town of Concord v. Boston Edison offers a vigorous statement of the position that in a regulated market, what may appear to be a price squeeze almost certainly cannot harm the competitive process and therefore should not be held to violate the antitrust laws. While not disputing the possibility of self-serving claims of price squeezes, this article shows that truly anticompetitive price squeezes may indeed occur in the electric power industry and cannot be so readily dismissed. This analysis begins with a brief factual and economic background on price squeezes, then addresses arguments made in Concord and elsewhere seeking to disprove their possibility, and demonstrate that sound economics and good policy require a more balanced approach

  16. Direct validation of atlas-based red nucleus identification for functional radiosurgery

    International Nuclear Information System (INIS)

    Stancanello, Joseph; Romanelli, Pantaleo; Sebastiano, Fabio; Modugno, Nicola; Muacevic, Alexander; Cerveri, Pietro; Esposito, Vincenzo; Ferrigno, Giancarlo; Uggeri, Fulvio; Cantore, Giampaolo

    2007-01-01

    Treatment targets in functional neurosurgery usually consist of selected structures within the thalamus and basal ganglia, which can be stimulated in order to affect specific brain pathways. Chronic electrical stimulation of these structures is a widely used approach for selected patients with advanced movement disorders. An alternative therapeutic solution consists of producing a lesion in the target nucleus, for example by means of radiosurgery, a noninvasive procedure, and this prevents the use of intraoperative microelectrode recording as a method for accurate target definition. The need to have accurate noninvasive localization of the target motivated our previous work on atlas-based identification; the aim of this present work is to provide additional validation of this approach based on the identification of the red nuclei (RN), which are located near the subthalamic nucleus (STN). Coordinates of RN were obtained from the Talairach and Tournoux (TT) atlas and transformed into the coordinates of the Montreal Neurological Institute (MNI) atlas, creating a mask representation of RN. The MNI atlas volume was nonrigidly registered onto the patient magnetic resonance imaging (MRI). This deformation field was then applied to the RN mask, providing its location on the patient MRI. Because RN are easily identifiable on 1.5 T T2-MRI images, they were manually delineated; the coordinates of the centers of mass of the manually and automatically identified structures were compared. Additionally, volumetric overlapping indices were calculated. Ten patients were examined by this technique. All indices indicated a high level of agreement between manually and automatically identified structures. These results not only confirm the accuracy of the method but also allow fine tuning of the automatic identification method to be performed

  17. Unilateral fusion of the odontoid process with the atlas in Klippel-Feil syndrome: a case report

    Energy Technology Data Exchange (ETDEWEB)

    Park, So Young; Ryu, Kyung Nam; Park, Ji Seon; Suk, Kyung Soo; Han, Mi Young [Kyunghee Medical Center, Seoul (Korea, Republic of)

    2006-07-15

    Klippel-Feil syndrome (KFS) displays congenital fusion of the cervical vertebrae; it is a relatively common condition and has many associated malformations such as Sprengel's deformity, scoliosis, rib anomalies, congenital defects of the brain or spinal cord, renal anomalies, congenital heart disease, deafness, cleft palate, cranial and facial asymmetry, and enteric cysts. There are various types of cervical fusion observed in KFS. However, fusion of the odontoid process with the atlas is a very rare finding. We report here on a 4-year-old boy with unilateral fusion of a separated odontoid process with the lateral mass of the atlas, and this was associated with a spontaneously closed ventricular septal defect, a small patent ductus arteriosus and a horseshoe kidney.

  18. File list: ALL.Lar.50.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. File list: ALL.Lar.20.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: ALL.Lar.05.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. File list: ALL.Lar.10.AllAg.Larval_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Lar.10.AllAg.Larval_brain dm3 All antigens Larvae Larval brain SRX1426945,SRX14...26944,SRX1426943,SRX1426946 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/ALL.Lar.10.AllAg.Larval_brain.bed ...

  2. Particulate Matter Resuspension in Mississippi Bight Evaluated with CONCORDE's Synthesis Model

    Science.gov (United States)

    O'Brien, S. J.; Quas, L. M.; Miles, T. N.; Pan, C.; Cambazoglu, M. K.; Soto Ramos, I. M.; Greer, A. T.; Church, I.; Wiggert, J. D.

    2017-12-01

    The CONsortium for oil spill exposure pathways in COastal River-Dominated Ecosystems (CONCORDE) was established to investigate the complex fine-scale biological, chemical and physical interactions in a marine system controlled by pulsed-river plume dynamics. During CONCORDE's spring 2016 field campaign, the In Situ Ichthyoplankton Imaging System (ISIIS) on the R/V Point Sur and the Scanfish on the R/V Pelican comprehensively characterized the physical and biological structure in the region. Increased suspended particulate matter was observed by the ISIIS, with concentrations at depth sufficient to completely occlude the in situ images of planktonic organisms. Data was also collected on the continental shelf during the spring cruise by the RU31 glider in the proximity of the Mississippi River Delta, east of the ISIIS / Scanfish transects. Backscatter and salinity observed by the Scanfish and glider showed elevated suspended particulate matter and increased salinity, suggesting a linkage to shoreward advection from the continental shelf of oceanic waters that are sufficiently energetic to drive sediment resuspension. As part of the CONCORDE research effort, a four-dimensional biogeochemical/lower trophic level synthesis model for Mississippi Sound and Bight has been developed, based on the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System. This study utilizes CONCORDE's synthesis model to investigate the physical forcing mechanisms affecting the increased suspended particulate matter concentration observed in the Mississippi Bight during spring 2016, and advection pathways between estuarine and shelf waters in the northern Gulf of Mexico. The results show that episodic, advection-driven resuspension is a critical aspect controlling suspended sediment distributions in Mississippi Bight, which has implications for observed spatio-temporal patterns of planktonic species.

  3. ATLAS. LHC experiments

    International Nuclear Information System (INIS)

    Anon.

    1995-01-01

    In Greek mythology, Atlas was a Titan who had to hold up the heavens with his hands as a punishment for having taken part in a revolt against the Olympians. For LHC, the ATLAS detector will also have an onerous physics burden to bear, but this is seen as a golden opportunity rather than a punishment. The major physics goal of CERN's LHC proton-proton collider is the quest for the long-awaited£higgs' mechanism which drives the spontaneous symmetry breaking of the electroweak Standard Model picture. The large ATLAS collaboration proposes a large general-purpose detector to exploit the full discovery potential of LHC's proton collisions. LHC will provide proton-proton collision luminosities at the aweinspiring level of 1034 cm2 s~1, with initial running in at 1033. The ATLAS philosophy is to handle as many signatures as possible at all luminosity levels, with the initial running providing more complex possibilities. The ATLAS concept was first presented as a Letter of Intent to the LHC Committee in November 1992. Following initial presentations at the Evian meeting (Towards the LHC Experimental Programme') in March of that year, two ideas for generalpurpose detectors, the ASCOT and EAGLE schemes, merged, with Friedrich Dydak (MPI Munich) and Peter Jenni (CERN) as ATLAS cospokesmen. Since the initial Letter of Intent presentation, the ATLAS design has been optimized and developed, guided by physics performance studies and the LHC-oriented detector R&D programme (April/May, page 3). The overall detector concept is characterized by an inner superconducting solenoid (for inner tracking) and large superconducting air-core toroids outside the calorimetry. This solution avoids constraining the calorimetry while providing a high resolution, large acceptance and robust detector. The outer magnet will extend over a length of 26 metres, with an outer diameter of almost 20 metres. The total weight of the detector is 7,000 tonnes. Fitted with its end

  4. Is There Concordance in Attitudes and Beliefs between Parents and Scientists about Autism Spectrum Disorder?

    Science.gov (United States)

    Fischbach, Ruth L.; Harris, Mark J.; Ballan, Michelle S.; Fischbach, Gerald D.; Link, Bruce G.

    2016-01-01

    There is no reported investigation comparing concordance in attitudes and beliefs about autism spectrum disorder between parents of children with autism spectrum disorder and scientists who research autism spectrum disorder. To investigate the level of concordance between these groups on causes of autism, priorities of research, perceived stigma,…

  5. Automated analysis of small animal PET studies through deformable registration to an atlas

    International Nuclear Information System (INIS)

    Gutierrez, Daniel F.; Zaidi, Habib

    2012-01-01

    This work aims to develop a methodology for automated atlas-guided analysis of small animal positron emission tomography (PET) data through deformable registration to an anatomical mouse model. A non-rigid registration technique is used to put into correspondence relevant anatomical regions of rodent CT images from combined PET/CT studies to corresponding CT images of the Digimouse anatomical mouse model. The latter provides a pre-segmented atlas consisting of 21 anatomical regions suitable for automated quantitative analysis. Image registration is performed using a package based on the Insight Toolkit allowing the implementation of various image registration algorithms. The optimal parameters obtained for deformable registration were applied to simulated and experimental mouse PET/CT studies. The accuracy of the image registration procedure was assessed by segmenting mouse CT images into seven regions: brain, lungs, heart, kidneys, bladder, skeleton and the rest of the body. This was accomplished prior to image registration using a semi-automated algorithm. Each mouse segmentation was transformed using the parameters obtained during CT to CT image registration. The resulting segmentation was compared with the original Digimouse atlas to quantify image registration accuracy using established metrics such as the Dice coefficient and Hausdorff distance. PET images were then transformed using the same technique and automated quantitative analysis of tracer uptake performed. The Dice coefficient and Hausdorff distance show fair to excellent agreement and a mean registration mismatch distance of about 6 mm. The results demonstrate good quantification accuracy in most of the regions, especially the brain, but not in the bladder, as expected. Normalized mean activity estimates were preserved between the reference and automated quantification techniques with relative errors below 10 % in most of the organs considered. The proposed automated quantification technique is

  6. Common Ground? The Concordance of Sarcopenia and Frailty Definitions

    NARCIS (Netherlands)

    Reijnierse, Esmee M.; Trappenburg, Marijke C.; Blauw, Gerard Jan; Verlaan, Sjors; de van der Schueren, Marian A.E.; Meskers, Carel G.M.; Maier, Andrea B.

    2016-01-01

    Objectives: This study aimed to explore the concordance between definitions of sarcopenia and frailty in a clinically relevant population of geriatric outpatients. Design: Data were retrieved from a cross-sectional study. Setting: The study was performed in a geriatric outpatient clinic of a

  7. ATLAS Grid Workflow Performance Optimization

    CERN Document Server

    Elmsheuser, Johannes; The ATLAS collaboration

    2018-01-01

    The CERN ATLAS experiment grid workflow system manages routinely 250 to 500 thousand concurrently running production and analysis jobs to process simulation and detector data. In total more than 300 PB of data is distributed over more than 150 sites in the WLCG. At this scale small improvements in the software and computing performance and workflows can lead to significant resource usage gains. ATLAS is reviewing together with CERN IT experts several typical simulation and data processing workloads for potential performance improvements in terms of memory and CPU usage, disk and network I/O. All ATLAS production and analysis grid jobs are instrumented to collect many performance metrics for detailed statistical studies using modern data analytics tools like ElasticSearch and Kibana. This presentation will review and explain the performance gains of several ATLAS simulation and data processing workflows and present analytics studies of the ATLAS grid workflows.

  8. Adapting Parcellation Schemes to Study Fetal Brain Connectivity in Serial Imaging Studies

    DEFF Research Database (Denmark)

    Cheng, Xi; Wilm, Jakob; Seshamani, Sharmishtaa

    2013-01-01

    A crucial step in studying brain connectivity is the definition of the Regions Of Interest (ROI's) which are considered as nodes of a network graph. These ROI's identified in structural imaging reflect consistent functional regions in the anatomies being compared. However in serial studies...... of the developing fetal brain such functional and associated structural markers are not consistently present over time. In this study we adapt two non-atlas based parcellation schemes to study the development of connectivity networks of a fetal monkey brain using Diffusion Weighted Imaging techniques. Results...... demonstrate that the fetal brain network exhibits small-world characteristics and a pattern of increased cluster coefficients and decreased global efficiency. These findings may provide a route to creating a new biomarker for healthy fetal brain development....

  9. Achieving Goal-Concordant Care: A Conceptual Model and Approach to Measuring Serious Illness Communication and Its Impact

    Science.gov (United States)

    Curtis, J. Randall; Tulsky, James A.

    2018-01-01

    Abstract Background: High-quality care for seriously ill patients aligns treatment with their goals and values. Failure to achieve “goal-concordant” care is a medical error that can harm patients and families. Because communication between clinicians and patients enables goal concordance and also affects the illness experience in its own right, healthcare systems should endeavor to measure communication and its outcomes as a quality assessment. Yet, little consensus exists on what should be measured and by which methods. Objectives: To propose measurement priorities for serious illness communication and its anticipated outcomes, including goal-concordant care. Methods: We completed a narrative review of the literature to identify links between serious illness communication, goal-concordant care, and other outcomes. We used this review to identify gaps and opportunities for quality measurement in serious illness communication. Results: Our conceptual model describes the relationship between communication, goal-concordant care, and other relevant outcomes. Implementation-ready measures to assess the quality of serious illness communication and care include (1) the timing and setting of serious illness communication, (2) patient experience of communication and care, and (3) caregiver bereavement surveys that include assessment of perceived goal concordance of care. Future measurement priorities include direct assessment of communication quality, prospective patient or family assessment of care concordance with goals, and assessment of the bereaved caregiver experience. Conclusion: Improving serious illness care necessitates ensuring that high-quality communication has occurred and measuring its impact. Measuring patient experience and receipt of goal-concordant care should be our highest priority. We have the tools to measure both. PMID:29091522

  10. Evaluating imaging-pathology concordance and discordance after ultrasound-guided breast biopsy

    Science.gov (United States)

    2018-01-01

    Ultrasound (US)-guided breast biopsy has become the main method for diagnosing breast pathology, and it has a high diagnostic accuracy, approaching that of open surgical biopsy. However, methods for confirming adequate lesion retrieval after US-guided biopsy are relatively limited and false-negative results are unavoidable. Determining imaging-pathology concordance after US-guided biopsy is essential for validating the biopsy result and providing appropriate management. In this review article, we briefly present the results of US-guided breast biopsy; describe general aspects to consider when establishing imaging-pathology concordance; and review the various categories of imaging-pathology correlations and corresponding management strategies. PMID:29169231

  11. Increasing Drought Sensitivity and Decline of Atlas Cedar (Cedrus atlantica in the Moroccan Middle Atlas Forests

    Directory of Open Access Journals (Sweden)

    Jesús Julio Camarero

    2011-09-01

    Full Text Available An understanding of the interactions between climate change and forest structure on tree growth are needed for decision making in forest conservation and management. In this paper, we investigated the relative contribution of tree features and stand structure on Atlas cedar (Cedrus atlantica radial growth in forests that have experienced heavy grazing and logging in the past. Dendrochronological methods were applied to quantify patterns in basal-area increment and drought sensitivity of Atlas cedar in the Middle Atlas, northern Morocco. We estimated the tree-to-tree competition intensity and quantified the structure in Atlas cedar stands with contrasting tree density, age, and decline symptoms. The relative contribution of tree age and size and stand structure to Atlas cedar growth decline was estimated by variance partitioning using partial-redundancy analyses. Recurrent drought events and temperature increases have been identified from local climate records since the 1970s. We detected consistent growth declines and increased drought sensitivity in Atlas cedar across all sites since the early 1980s. Specifically, we determined that previous growth rates and tree age were the strongest tree features, while Quercus rotundifolia basal area was the strongest stand structure measure related to Atlas cedar decline. As a result, we suggest that Atlas cedar forests that have experienced severe drought in combination with grazing and logging may be in the process of shifting dominance toward more drought-tolerant species such as Q. rotundifolia.

  12. A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (Saimiri sciureus) based on diffusion tensor imaging.

    Science.gov (United States)

    Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S; Ding, Zhaohua; Gore, John C; Chen, Li Min; Landman, Bennett A; Anderson, Adam W

    2016-02-27

    Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

  13. A 3D high resolution ex vivo white matter atlas of the common squirrel monkey (saimiri sciureus) based on diffusion tensor imaging

    Science.gov (United States)

    Gao, Yurui; Parvathaneni, Prasanna; Schilling, Kurt G.; Wang, Feng; Stepniewska, Iwona; Xu, Zhoubing; Choe, Ann S.; Ding, Zhaohua; Gore, John C.; Chen, Li min; Landman, Bennett A.; Anderson, Adam W.

    2016-03-01

    Modern magnetic resonance imaging (MRI) brain atlases are high quality 3-D volumes with specific structures labeled in the volume. Atlases are essential in providing a common space for interpretation of results across studies, for anatomical education, and providing quantitative image-based navigation. Extensive work has been devoted to atlas construction for humans, macaque, and several non-primate species (e.g., rat). One notable gap in the literature is the common squirrel monkey - for which the primary published atlases date from the 1960's. The common squirrel monkey has been used extensively as surrogate for humans in biomedical studies, given its anatomical neuro-system similarities and practical considerations. This work describes the continued development of a multi-modal MRI atlas for the common squirrel monkey, for which a structural imaging space and gray matter parcels have been previously constructed. This study adds white matter tracts to the atlas. The new atlas includes 49 white matter (WM) tracts, defined using diffusion tensor imaging (DTI) in three animals and combines these data to define the anatomical locations of these tracks in a standardized coordinate system compatible with previous development. An anatomist reviewed the resulting tracts and the inter-animal reproducibility (i.e., the Dice index of each WM parcel across animals in common space) was assessed. The Dice indices range from 0.05 to 0.80 due to differences of local registration quality and the variation of WM tract position across individuals. However, the combined WM labels from the 3 animals represent the general locations of WM parcels, adding basic connectivity information to the atlas.

  14. Integrating Networking into ATLAS

    CERN Document Server

    Mc Kee, Shawn Patrick; The ATLAS collaboration

    2018-01-01

    Networking is foundational to the ATLAS distributed infrastructure and there are many ongoing activities related to networking both within and outside of ATLAS. We will report on the progress in a number of areas exploring ATLAS's use of networking and our ability to monitor the network, analyze metrics from the network, and tune and optimize application and end-host parameters to make the most effective use of the network. Specific topics will include work on Open vSwitch for production systems, network analytics, FTS testing and tuning, and network problem alerting and alarming.

  15. ATLAS End-cap Part II

    CERN Multimedia

    2007-01-01

    The epic journey of the ATLAS magnets is drawing to an end. On Thursday 12 July, the second end-cap of the ATLAS toroid magnet was lowered into the cavern of the experiment with the same degree of precision as the first (see Bulletin No. 26/2007). This spectacular descent of the 240-tonne component, is one of the last transport to be completed for ATLAS.

  16. ATLAS experiment : mapping the secrets of the universe

    CERN Multimedia

    ATLAS Outreach

    2010-01-01

    This 4 page color brochure describes ATLAS and the LHC, the ATLAS inner detector, calorimeters, muon spectrometer, magnet system, a short definition of the terms "particles," "dark matter," "mass," "antimatter." It also explains the ATLAS collaboration and provides the ATLAS website address with some images of the detector and the ATLAS collaboration at work.

  17. Concordance of sleep and pain outcomes of diverse interventions: an umbrella review.

    Directory of Open Access Journals (Sweden)

    Anthony G Doufas

    Full Text Available BACKGROUND/OBJECTIVE: Pain influences sleep and vice versa. We performed an umbrella review of meta-analyses on treatments for diverse conditions in order to examine whether diverse medical treatments for different conditions have similar or divergent effects on pain and sleep. METHODS: We searched published systematic reviews with meta-analyses in the Cochrane Database of Systematic Reviews until October 20, 2011. We identified randomized trials (or meta-analyses thereof, when >1 trial was available where both pain and sleep outcomes were examined. Pain outcomes were categorized as headache, musculoskeletal, abdominal, pelvic, generic or other pain. Sleep outcomes included insomnia, sleep disruption, and sleep disturbance. We estimated odds ratios for all outcomes and evaluated the concordance in the direction of effects between sleep and various types of pain and the correlation of treatment effects between sleep and pain outcomes. RESULTS: 151 comparisons with 385 different trials met our eligibility criteria. 96 comparisons had concordant direction of effects between each pain outcome and sleep, while in 55 the effect estimates were in opposite directions (P<0.0001. In the 20 comparisons with largest amount of evidence, the experimental drug always had worse sleep outcomes and tended to have worse pain outcomes in 17/20 cases. For headache and musculoskeletal pain, 69 comparisons showed concordant direction of effects with sleep outcomes and 36 showed discordant direction (P<0.0001. For the other 4 pain types there were overall 27 vs. 19 pairs with concordant vs. discordant direction of effects (P = 0.095. There was a weak correlation of the treatment effect sizes for sleep vs. headache/musculoskeletal pain (r = 0.17, P = 0.092. CONCLUSIONS: Medical interventions tend to have effects in the same direction for pain and sleep outcomes, but exceptions occur. Concordance is primarily seen for sleep and headache or musculoskeletal

  18. File list: NoD.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  19. File list: NoD.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  20. File list: NoD.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  1. File list: NoD.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  2. File list: InP.Neu.20.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  3. File list: InP.Neu.50.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  4. File list: InP.Neu.05.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: InP.Neu.10.AllAg.Brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available InP.Neu.10.AllAg.Brain mm9 Input control Neural Brain SRX236086,ERX279248,ERX279249...513118,ERX1027841,ERX1027839,ERX1027840,SRX150261,ERX513117 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/InP.Neu.10.AllAg.Brain.bed ...

  6. ATLAS Visitors Centre

    CERN Multimedia

    claudia Marcelloni

    2009-01-01

    ATLAS Visitors Centre has opened its shiny new doors to the public. Officially launched on Monday February 23rd, 2009, the permanent exhibition at Point 1 was conceived as a tour resource for ATLAS guides, and as a way to preserve the public’s opportunity to get a close-up look at the experiment in action when the cavern is sealed.

  7. ATLAS rewards industry

    CERN Document Server

    Maximilien Brice

    2006-01-01

    For contributing vital pieces to the ATLAS puzzle, three industries were recognized on Friday 5 May during a supplier awards ceremony. After a welcome and overview of the ATLAS experiment by spokesperson Peter Jenni, CERN Secretary-General Maximilian Metzger stressed the importance of industry to CERN's scientific goals. Picture 30 : representatives of the three award-wining companies after the ceremony

  8. The ATLAS Experiment Laboratory - Overview

    International Nuclear Information System (INIS)

    Malecki, P.

    1999-01-01

    Full text: ATLAS Experiment Laboratory has been created by physicists and engineers preparing a research programme and detector for the LHC collider. This group is greatly supported by members of other Departments taking also part (often full time) in the ATLAS project. These are: J. Blocki, J. Godlewski, Z. Hajduk, P. Kapusta, B. Kisielewski, W. Ostrowicz, E. Richter-Was, and M. Turala. Our ATLAS Laboratory realizes its programme in very close collaboration with the Faculty of Physics and Nuclear Technology of the University of Mining and Metallurgy. ATLAS, A Toroidal LHC ApparatuS Collaboration groups about 1700 experimentalists from about 150 research institutes. This apparatus, a huge system of many detectors, which are technologically very advanced, is going to be ready by 2005. With the start of the 2 x 7 TeV LHC collider ATLAS and CMS (the sister experiment at LHC) will begin their fascinating research programme at beam energies and intensities which have never been exploited. (author)

  9. ATLAS Award for Difficult Task

    CERN Multimedia

    2004-01-01

    Two Russian companies were honoured with an ATLAS Award, for supply of the ATLAS Inner Detector barrel support structure elements, last week. On 23 March the Russian company ORPE Technologiya and its subcontractor, RSP Khrunitchev, were jointly presented with an ATLAS Supplier Award. Since 1998, ORPE Technologiya has been actively involved in the development of the carbon-fibre reinforced plastic elements of the ATLAS Inner Detector barrel support structure. After three years of joint research and development, CERN and ORPE Technologiya launched the manufacturing contract. It had a tight delivery schedule and very demanding specifications in terms of mechanical tolerance and stability. The contract was successfully completed with the arrival of the last element of the structure at CERN on 8 January 2004. The delivery of this key component of the Inner Detector deserves an ATLAS Award given the difficulty of manufacturing the end-frames, which very few companies in the world would have been able to do at an ...

  10. ATLAS & Google - The Data Ocean Project

    CERN Document Server

    Lassnig, Mario; The ATLAS collaboration

    2018-01-01

    With the LHC High Luminosity upgrade the workload and data management systems are facing new major challenges. To address those challenges ATLAS and Google agreed to cooperate on a project to connect Google Cloud Storage and Compute Engine to the ATLAS computing environment. The idea is to allow ATLAS to explore the use of different computing models, to allow ATLAS user analysis to benefit from the Google infrastructure, and to give Google real science use cases to improve their cloud platform. Making the output of a distributed analysis from the grid quickly available to the analyst is a difficult problem. Redirecting the analysis output to Google Cloud Storage can provide an alternative, faster solution for the analyst. First, Google's Cloud Storage will be connected to the ATLAS Data Management System Rucio. The second part aims to let jobs run on Google Compute Engine, accessing data from either ATLAS storage or Google Cloud Storage. The third part involves Google implementing a global redirection between...

  11. A Comparison of Total Antioxidant Capacities of Concord, Purple, Red, and Green Grapes Using the CUPRAC Assay

    Directory of Open Access Journals (Sweden)

    Connor M. Callaghan

    2013-10-01

    Full Text Available Considering how popular grapes are in terms of their antioxidant benefits, we compared concord, purple, red, and green grapes for total antioxidant capacity (TAC and carbohydrate concentration. All grapes were acquired from commercial sources and samples of each were separated into skinned and not skinned groups. Each whole grape and the skins were individually homogenized and then separated into pulp and supernatant fractions. Each fraction was analyzed for total TAC and carbohydrates. The concord grapes and purple grapes had significantly higher TAC in the homogenates than did the red or green grapes. The concord grapes and green grapes had significantly higher TAC in the pulp than in the cytosol whereas the red and purple grapes had approximately the same amount. The majority of the TAC of the purple and red grapes was in the skin whereas the concord and green grapes had approximately the same TAC in the skin and pulp. The concord and purple grapes had the highest TAC when compared to the red and green grapes, whereas the red and green grapes had approximately the same total TAC.

  12. The ATLAS hadronic tau trigger

    International Nuclear Information System (INIS)

    Shamim, Mansoora

    2012-01-01

    The extensive tau physics programs of the ATLAS experiment relies heavily on trigger to select hadronic decays of tau lepton. Such a trigger is implemented in ATLAS to efficiently collect signal events, while keeping the rate of multi-jet background within the allowed bandwidth. This contribution summarizes the performance of the ATLAS hadronic tau trigger system during 2011 data taking period and improvements implemented for the 2012 data collection.

  13. ATLAS OF EUROPEAN VALUES

    NARCIS (Netherlands)

    M Ed Uwe Krause

    2008-01-01

    Uwe Krause: Atlas of Eurpean Values De Atlas of European Values is een samenwerkingsproject met bijbehorende website van de Universiteit van Tilburg en Fontys Lerarenopleiding in Tilburg, waarbij de wetenschappelijke data van de European Values Study (EVS) voor het onderwijs toegankelijk worden

  14. ATLAS brochure (Italian version)

    CERN Multimedia

    Lefevre, C

    2010-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  15. ATLAS brochure (French version)

    CERN Multimedia

    Lefevre, C

    2012-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  16. ATLAS brochure (German version)

    CERN Multimedia

    Lefevre, C

    2012-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  17. ATLAS brochure (Danish version)

    CERN Multimedia

    Lefevre, C

    2010-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  18. An autoradiographic map of (3H)diprenorphine binding in rat brain: effects of social interaction

    International Nuclear Information System (INIS)

    Panksepp, J.; Bishop, P.

    1981-01-01

    (3H)Diprenorphine binding was analyzed autoradiographically in the brains of 33 day old rat pups. A photographic atlas of diprenorphine binding in the coronal plane is provided to highlight the dispersion of opioid receptor systems through the brain. To determine whether brain opioid release may be induced by social interactions, half the animals were sacrificed following a 30 min period of social interaction while the other half were sacrificed following 30 min of social isolation. Opioid binding was higher in isolate-tested animals than socially-tested ones, suggesting that social interaction may promote endogenous brain opioid release

  19. Effects of deformable registration algorithms on the creation of statistical maps for preoperative targeting in deep brain stimulation procedures

    Science.gov (United States)

    Liu, Yuan; D'Haese, Pierre-Francois; Dawant, Benoit M.

    2014-03-01

    Deep brain stimulation, which is used to treat various neurological disorders, involves implanting a permanent electrode into precise targets deep in the brain. Accurate pre-operative localization of the targets on pre-operative MRI sequence is challenging as these are typically located in homogenous regions with poor contrast. Population-based statistical atlases can assist with this process. Such atlases are created by acquiring the location of efficacious regions from numerous subjects and projecting them onto a common reference image volume using some normalization method. In previous work, we presented results concluding that non-rigid registration provided the best result for such normalization. However, this process could be biased by the choice of the reference image and/or registration approach. In this paper, we have qualitatively and quantitatively compared the performance of six recognized deformable registration methods at normalizing such data in poor contrasted regions onto three different reference volumes using a unique set of data from 100 patients. We study various metrics designed to measure the centroid, spread, and shape of the normalized data. This study leads to a total of 1800 deformable registrations and results show that statistical atlases constructed using different deformable registration methods share comparable centroids and spreads with marginal differences in their shape. Among the six methods being studied, Diffeomorphic Demons produces the largest spreads and centroids that are the furthest apart from the others in general. Among the three atlases, one atlas consistently outperforms the other two with smaller spreads for each algorithm. However, none of the differences in the spreads were found to be statistically significant, across different algorithms or across different atlases.

  20. White matter differences in monozygotic twins discordant or concordant for obsessive-compulsive symptoms: a combined diffusion tensor imaging/voxel-based morphometry study.

    Science.gov (United States)

    den Braber, Anouk; van 't Ent, Dennis; Boomsma, Dorret I; Cath, Danielle C; Veltman, Dick J; Thompson, Paul M; de Geus, Eco J C

    2011-11-15

    Neuroimaging studies of obsessive-compulsive disorder (OCD) patients point to deficits in cortico-striato-thalamo-cortical circuits that might include changes in white matter. The contribution of environmental and genetic factors to the various OCD-related changes in brain structures remains to be established. White matter structures were analyzed in 140 subjects with both diffusion tensor imaging and voxel-based morphometry. We studied 20 monozygotic twin pairs discordant for obsessive-compulsive symptoms (OCS) to detect the effects of environmental risk factors for obsessive-compulsive (OC) symptomatology. Furthermore, we compared 28 monozygotic twin pairs concordant for low OCS scores with 23 twin pairs concordant for high OCS scores to detect the effects of genetic risk factors for OC symptomatology. Discordant pair analysis showed that the environmental risk was associated with an increase in dorsolateral-prefrontal white matter. Analysis of concordant pairs showed that the genetic risk was associated with a decrease in inferior frontal white matter. Various white matter tracts showed opposite effects of environmental and genetic risk factors (e.g., right medial frontal, left parietal, and right middle temporal), illustrating the need for designs that separate these classes of risk factors. Different white matter regions were affected by environmental and genetic risk factors for OC symptomatology, but both classes of risk factors might, in aggregate, create an imbalance between the indirect loop of the cortico-striato-thalamo-cortical network (to the dorsolateral-prefrontal region)-important for inhibition and switching between behaviors-and the direct loop (involving the inferior frontal region) that contributes to the initiation and continuation of behaviors. Copyright © 2011 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  1. File list: His.Neu.20.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.20.AllAg.Fetal_brain hg19 Histone Neural Fetal brain SRX860887,SRX860879,SR...X860886,SRX860883,SRX860881,SRX860885,SRX860884,SRX860880,SRX860888,SRX860882 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.20.AllAg.Fetal_brain.bed ...

  2. File list: His.Neu.05.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.05.AllAg.Fetal_brain hg19 Histone Neural Fetal brain SRX860887,SRX860886,SR...X860885,SRX860881,SRX860879,SRX860888,SRX860880,SRX860883,SRX860884,SRX860882 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.05.AllAg.Fetal_brain.bed ...

  3. File list: His.Neu.10.AllAg.Fetal_brain [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Neu.10.AllAg.Fetal_brain hg19 Histone Neural Fetal brain SRX860887,SRX860886,SR...X860879,SRX860888,SRX860880,SRX860881,SRX860885,SRX860883,SRX860884,SRX860882 http://dbarchive.biosciencedbc.jp/kyushu-u/hg19/assembled/His.Neu.10.AllAg.Fetal_brain.bed ...

  4. Last piece of the puzzle for ATLAS

    CERN Multimedia

    Clare Ryan

    At around 15.40 on Friday 29th February the ATLAS collaboration cracked open the champagne as the second of the small wheels was lowered into the cavern. Each of ATLAS' small wheels are 9.3 metres in diameter and weigh 100 tonnes including the massive shielding elements. They are the final parts of ATLAS' muon spectrometer. The first piece of ATLAS was installed in 2003 and since then many detector elements have journeyed down the 100 metre shaft into the ATLAS underground cavern. This last piece completes this gigantic puzzle.

  5. NATIONAL ATLAS OF THE ARCTIC

    Directory of Open Access Journals (Sweden)

    Nikolay S. Kasimov

    2018-01-01

    Full Text Available The National Atlas of the Arctic is a set of spatio-temporal information about the geographic, ecological, economic, historical-ethnographic, cultural, and social features of theArcticcompiled as a cartographic model of the territory. The Atlas is intended for use in a wide range of scientific, management, economic, defense, educational, and public activities. The state policy of theRussian Federationin the Arctic for the period until 2020 and beyond, states that the Arctic is of strategic importance forRussiain the 21st century. A detailed description of all sections of the Atlas is given. The Atlas can be used as an information-reference and educational resource or as a gift edition.

  6. Normal feline brain: clinical anatomy using magnetic resonance imaging.

    Science.gov (United States)

    Mogicato, G; Conchou, F; Layssol-Lamour, C; Raharison, F; Sautet, J

    2012-04-01

    The purpose of this study was to provide a clinical anatomy atlas of the feline brain using magnetic resonance imaging (MRI). Brains of twelve normal cats were imaged using a 1.5 T magnetic resonance unit and an inversion/recovery sequence (T1). Fourteen relevant MRI sections were chosen in transverse, dorsal, median and sagittal planes. Anatomic structures were identified and labelled using anatomical texts and Nomina Anatomica Veterinaria, sectioned specimen heads, and previously published articles. The MRI sections were stained according to the major embryological and anatomical subdivisions of the brain. The relevant anatomical structures seen on MRI will assist clinicians to better understand MR images and to relate this neuro-anatomy to clinical signs. © 2011 Blackwell Verlag GmbH.

  7. EnviroAtlas Proximity to Parks Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset shows...

  8. Mapping social behavior-induced brain activation at cellular resolution in the mouse

    Science.gov (United States)

    Kim, Yongsoo; Venkataraju, Kannan Umadevi; Pradhan, Kith; Mende, Carolin; Taranda, Julian; Turaga, Srinivas C.; Arganda-Carreras, Ignacio; Ng, Lydia; Hawrylycz, Michael J.; Rockland, Kathleen; Seung, H. Sebastian; Osten, Pavel

    2014-01-01

    Understanding how brain activation mediates behaviors is a central goal of systems neuroscience. Here we apply an automated method for mapping brain activation in the mouse in order to probe how sex-specific social behaviors are represented in the male brain. Our method uses the immediate early gene c-fos, a marker of neuronal activation, visualized by serial two-photon tomography: the c-fos-GFP-positive neurons are computationally detected, their distribution is registered to a reference brain and a brain atlas, and their numbers are analyzed by statistical tests. Our results reveal distinct and shared female and male interaction-evoked patterns of male brain activation representing sex discrimination and social recognition. We also identify brain regions whose degree of activity correlates to specific features of social behaviors and estimate the total numbers and the densities of activated neurons per brain areas. Our study opens the door to automated screening of behavior-evoked brain activation in the mouse. PMID:25558063

  9. Impact of Patient-Provider Race, Ethnicity, and Gender Concordance on Cancer Screening: Findings from Medical Expenditure Panel Survey.

    Science.gov (United States)

    Malhotra, Jyoti; Rotter, David; Tsui, Jennifer; Llanos, Adana A M; Balasubramanian, Bijal A; Demissie, Kitaw

    2017-12-01

    Background: Racial and ethnic minorities experience lower rates of cancer screening compared with non-Hispanic whites (NHWs). Previous studies evaluating the role of patient-provider race, ethnicity, or gender concordance in cancer screening have been inconclusive. Methods: In a cross-sectional analysis using the Medical Expenditure Panel Survey (MEPS), data from 2003 to 2010 were assessed for associations between patient-provider race, ethnicity, and/or gender concordance and, screening (American Cancer Society guidelines) for breast, cervical, and colorectal cancer. Multivariable logistic analyses were conducted to examine associations of interest. Results: Of the 32,041 patient-provider pairs in our analysis, more than 60% of the patients were NHW, 15% were non-Hispanic black (NHB), and 15% were Hispanic. Overall, patients adherent to cancer screening were more likely to be non-Hispanic, better educated, married, wealthier, and privately insured. Patient-provider gender discordance was associated with lower rates of breast [OR, 0.83; 95% confidence interval (CI), 0.76-0.90], cervical (OR, 0.83; 95% CI, 0.76-0.91), and colorectal cancer (OR, 0.84; 95% CI, 0.79-0.90) screening in all patients. This association was also significant after adjusting for racial and/or ethnic concordance. Conversely, among NHWs and NHBs, patient-provider racial and/or ethnic concordance was not associated with screening. Among Hispanics, patient-provider ethnic discordant pairs had higher breast (58% vs. 52%) and colorectal cancer (45% vs. 39%) screening rates compared with concordant pairs. Conclusions: Patient-provider gender concordance positively affected cancer screening. Patient-provider ethnic concordance was inversely associated with receipt of cancer screening among Hispanics. This counter-intuitive finding requires further study. Impact: Our findings highlight the importance of gender concordance in improving cancer screening rates. Cancer Epidemiol Biomarkers Prev; 26

  10. Development, deployment and operations of ATLAS databases

    International Nuclear Information System (INIS)

    Vaniachine, A. V.; von der Schmitt, J. G.

    2008-01-01

    In preparation for ATLAS data taking, a coordinated shift from development towards operations has occurred in ATLAS database activities. In addition to development and commissioning activities in databases, ATLAS is active in the development and deployment (in collaboration with the WLCG 3D project) of the tools that allow the worldwide distribution and installation of databases and related datasets, as well as the actual operation of this system on ATLAS multi-grid infrastructure. We describe development and commissioning of major ATLAS database applications for online and offline. We present the first scalability test results and ramp-up schedule over the initial LHC years of operations towards the nominal year of ATLAS running, when the database storage volumes are expected to reach 6.1 TB for the Tag DB and 1.0 TB for the Conditions DB. ATLAS database applications require robust operational infrastructure for data replication between online and offline at Tier-0, and for the distribution of the offline data to Tier-1 and Tier-2 computing centers. We describe ATLAS experience with Oracle Streams and other technologies for coordinated replication of databases in the framework of the WLCG 3D services

  11. 123I-iomazenil brain receptor SPECT in focal epilepsy. In comparison with 99mTc-HMPAO brain SPECT, MRI and Video/EEG monitoring

    International Nuclear Information System (INIS)

    Xu Hao; Wang Tongge; Huang Li; Michael Cordes

    1998-01-01

    Purpose: To evaluate the clinical value of 123 I-Iomazenil brain receptor SPECT in diagnosis of focal epilepsy in comparison with 99m Tc-HMPAO brain SPECT, MRI and Video/EEG monitoring. Methods 123 I-Iomazenil brain receptor SPECT was performed on 40 patients with focal epilepsy. The results were compared with those obtained by 99m Tc-HMPAO brain SPECT, MRI and Video/EEG monitoring. Results: In 40 patients, the sensitivity of Video/EEG monitoring for localization of epileptogenic area was 95% (38/40). The sensitivity of 123 I-iomazenil brain receptor SPECT, 99m Tc-HMPAO brain SPECT and MRI for localization of epileptogenic area compared with Video/EEG monitoring ('gold standard') was 65.8%(25/38), 55.3%(21/38) and 47.4%(18/38), respectively. The localization of epileptogenic area with 123 I-Iomazenil brain receptor SPECT was in concordance with Video/EEG monitoring in 20 patients, 99m Tc-HMPAO brain SPECT in 15 patients and MRI in 16 patients, respectively. The sensitivity of 123 I-Iomazenil brain receptor SPECT combined with MRI for localization of epileptogenic area was 84.2%(32/38). Conclusions: 123 I-Iomazenil brain receptor SPECT is a useful method in detecting and localizing epileptogenic area. The combination of 123 I-Iomazenil brain receptor SPECT and MRI has a high sensitivity for detecting epileptogenic area

  12. Adherence to Cardiovascular Disease Medications: Does Patient-Provider Race/Ethnicity and Language Concordance Matter?

    OpenAIRE

    Traylor, Ana H.; Schmittdiel, Julie A.; Uratsu, Connie S.; Mangione, Carol M.; Subramanian, Usha

    2010-01-01

    BACKGROUND: Patient-physician race/ethnicity and language concordance may improve medication adherence and reduce disparities in cardiovascular disease (CVD) by fostering trust and improved patient-physician communication. OBJECTIVE: To examine the association of patient race/ethnicity and language and patient-physician race/ethnicity and language concordance on medication adherence rates for a large cohort of diabetes patients in an integrated delivery system. DESIGN: We studied 131,277 adul...

  13. ATLAS

    Data.gov (United States)

    Federal Laboratory Consortium — ATLAS is a particle physics experiment at the Large Hadron Collider at CERN, the European Organization for Nuclear Research. Scientists from Brookhaven have played...

  14. Concordance between macrophytes and macroinvertebrates in a Mediterranean river of central Apennine region.

    Science.gov (United States)

    Traversetti, Lorenzo; Scalici, Massimiliano; Ginepri, Valeria; Manfrin, Alessandro; Ceschin, Simona

    2014-05-01

    The main aim of this study was to improve the knowledge about the concordance among macrophytes and macroinvertebrates to provide complementary information and facilitate the procedures for quality assessment of river ecosystems. Macrophytes and macroinvertebrates were collected in 11 sampling sites along a central Apennine calcareous river in October 2008 and June 2009. The concordance between the two biomonitoring groups was tested according to several environmental parameters. The comparison of data matrix similarities by Mantel test showed differences in the assemblage of macrophytes and macroinvertebrates along the river since correlation values were 0.04, p > 0.05 in October 2008 and 0.39, p > 0.05 in June 2009. The study revealed lack of concordance between the two groups, emphasizing that the information provided by macrophytes and macroinvertebrates does not overlap in terms of response to environmental parameters. Indeed, the two different biological groups resulted useful descriptors of different parameters. Together, they could represent a complementary tool to reflect the river environmental quality.

  15. ATLAS brochure (Norwegian version)

    CERN Multimedia

    Lefevre, C

    2009-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter. Français

  16. A Slice of ATLAS

    CERN Document Server

    2004-01-01

    An entire section of the ATLAS detector is being assembled at Prévessin. Since May the components have been tested using a beam from the SPS, giving the ATLAS team valuable experience of operating the detector as well as an opportunity to debug the system.

  17. Utah optrode array customization using stereotactic brain atlases and 3-D CAD modeling for optogenetic neocortical interrogation in small rodents and nonhuman primates.

    Science.gov (United States)

    Boutte, Ronald W; Merlin, Sam; Yona, Guy; Griffiths, Brandon; Angelucci, Alessandra; Kahn, Itamar; Shoham, Shy; Blair, Steve

    2017-10-01

    As the optogenetic field expands, the need for precise targeting of neocortical circuits only grows more crucial. This work demonstrates a technique for using Solidworks ® computer-aided design (CAD) and readily available stereotactic brain atlases to create a three-dimensional (3-D) model of the dorsal region of area visual cortex 4 (V4D) of the macaque monkey ( Macaca fascicularis ) visual cortex. The 3-D CAD model of the brain was used to customize an [Formula: see text] Utah optrode array (UOA) after it was determined that a high-density ([Formula: see text]) UOA caused extensive damage to marmoset ( Callithrix jacchus ) primary visual cortex as assessed by electrophysiological recording of spiking activity through a 1.5-mm-diameter through glass via. The [Formula: see text] UOA was customized for optrode length ([Formula: see text]), optrode width ([Formula: see text]), optrode pitch ([Formula: see text]), backplane thickness ([Formula: see text]), and overall form factor ([Formula: see text]). Two [Formula: see text] UOAs were inserted into layer VI of macaque V4D cortices with minimal damage as assessed in fixed tissue cytochrome oxidase staining in nonrecoverable surgeries. Additionally, two [Formula: see text] arrays were implanted in mice ( Mus musculus ) motor cortices, providing early evidence for long-term tolerability (over 6 months), and for the ability to integrate the UOA with a Holobundle light delivery system toward patterned optogenetic stimulation of cortical networks.

  18. The Latest from ATLAS

    CERN Multimedia

    2009-01-01

    Since November 2008, ATLAS has undertaken detailed maintenance, consolidation and repair work on the detector (see Bulletin of 20 July 2009). Today, the fraction of the detector that is operational has increased compared to last year: less than 1% of dead channels for most of the sub-systems. "We are going to start taking data this year with a detector which is even more efficient than it was last year," agrees ATLAS Spokesperson, Fabiola Gianotti. By mid-September the detector was fully closed again, and the cavern sealed. The magnet system has been operated at nominal current for extensive periods over recent months. Once the cavern was sealed, ATLAS began two weeks of combined running. Right now, subsystems are joining the run incrementally until the point where the whole detector is integrated and running as one. In the words of ATLAS Technical Coordinator, Marzio Nessi: "Now we really start physics." In parallel, the analysis ...

  19. A thermosiphon for ATLAS

    CERN Multimedia

    Rosaria Marraffino

    2013-01-01

    A new thermosiphon cooling system, designed for the ATLAS silicon detectors by CERN’s EN-CV team in collaboration with the experiment, will replace the current system in the next LHC run in 2015. Using the basic properties of density difference and making gravity do the hard work, the thermosiphon promises to be a very reliable solution that will ensure the long-term stability of the whole system.   Former compressor-based cooling system of the ATLAS inner detectors. The system is currently being replaced by the innovative thermosiphon. (Photo courtesy of Olivier Crespo-Lopez). Reliability is the major issue for the present cooling system of the ATLAS silicon detectors. The system was designed 13 years ago using a compressor-based cooling cycle. “The current cooling system uses oil-free compressors to avoid fluid pollution in the delicate parts of the silicon detectors,” says Michele Battistin, EN-CV-PJ section leader and project leader of the ATLAS thermosiphon....

  20. The High-Resolution IRAS Galaxy Atlas

    Science.gov (United States)

    Cao, Yu; Terebey, Susan; Prince, Thomas A.; Beichman, Charles A.; Oliversen, R. (Technical Monitor)

    1997-01-01

    An atlas of the Galactic plane (-4.7 deg is less than b is less than 4.7 deg), along with the molecular clouds in Orion, rho Oph, and Taurus-Auriga, has been produced at 60 and 100 microns from IRAS data. The atlas consists of resolution-enhanced co-added images with 1 min - 2 min resolution and co-added images at the native IRAS resolution. The IRAS Galaxy Atlas, together with the Dominion Radio Astrophysical Observatory H(sub I) line/21 cm continuum and FCRAO CO (1-0) Galactic plane surveys, which both have similar (approx. 1 min) resolution to the IRAS atlas, provides a powerful tool for studying the interstellar medium, star formation, and large-scale structure in our Galaxy. This paper documents the production and characteristics of the atlas.