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on page 1 showing 20 out of 624 results

Cite this (1000 Functional Connectomes Project, RRID:SCR_005361)

URL: http://fcon_1000.projects.nitrc.org/

Resource Type: Resource, database, image collection, catalog, service resource, storage service resource, image repository, data repository, data or information resource

Database of resting state fMRI (R-fMRI) datasets collected from sites around the world. It demonstrates open sharing of R-fMRI data and aims to emphasize the aggregation and sharing of well-phenotyped datasets.

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    3DBar

Cite this (3DBar, RRID:SCR_008896)

URL: http://www.3dbar.org

Resource Type: Resource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resource

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

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    3D Brain

Cite this (3D Brain, RRID:SCR_013138)

URL: https://itunes.apple.com/be/app/3d-brain/id331399332?mt=8

Resource Type: Resource, software application, narrative resource, training material, software resource, mobile app, data or information resource

iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later.

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Cite this (3D surgical atlases of the murine head, RRID:SCR_008039)

URL: http://phm.utoronto.ca/~jeffh/surgical.htm

Resource Type: Resource, atlas, data or information resource

3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system.

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Cite this (499 fROI atlas, RRID:SCR_014756)

URL: http://findlab.stanford.edu/functional_ROIs.html

Resource Type: Resource, atlas, data or information resource

Atlas of functional ROIs (fROIs) containing 499 regions, with extensive gray matter coverage. Atlases are available for download directly from the website.

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Cite this (4D Atlases Construction, RRID:SCR_002227)

URL: http://www.med.unc.edu/bric/ideagroup/free-softwares/4d-atlases-construction

Resource Type: Resource, software resource

Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications.

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Cite this (7T Structural MRI scans ATAG, RRID:SCR_014084)

URL: http://www.nitrc.org/projects/atag_mri_scans/

Resource Type: Resource, data set, atlas, data or information resource

Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases.

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Cite this (90 fROI atlas, RRID:SCR_014757)

URL: http://findlab.stanford.edu/functional_ROIs.html

Resource Type: Resource, atlas, data or information resource

Atlas of functional ROI's, including individual networks (auditory network, sensorimotor network, etc.). Atlases of individual networks and combined networks are available for download directly from the website.

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Cite this (ABC (Atlas Based Classification), RRID:SCR_005981)

URL: http://www.nitrc.org/projects/abc

Resource Type: Resource, software resource, image analysis software, workflow software, data processing software, software application

A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.

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Cite this (ABCDreport, RRID:SCR_016030)

URL: https://github.com/ABCD-STUDY/ABCDreport

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software application as a simple system to review study progress. Used in ABCD study.

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    aBEAT

Cite this (aBEAT, RRID:SCR_002238)

URL: http://www.med.unc.edu/bric/ideagroup/free-softwares/abeat-a-toolbox-for-consistent-analysis-of-longitudinal-adult-brain-mri

Resource Type: Resource, image analysis software, data processing software, software application, software resource, software toolkit, image processing software

A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

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Cite this (Accelerating Medicines Partnership - Alzheimers, RRID:SCR_003742)

URL: http://www.nih.gov/science/amp/alzheimers.htm

Resource Type: Resource, organization portal, portal, consortium, data or information resource

The Alzheimer's disease arm of the Accelerating Medicines Partnership (AMP) that will identify biomarkers that can predict clinical outcomes, conduct a large scale analysis of human AD patient brain tissue samples to validate biological targets, and to increase the understanding of molecular pathways involved in the disease to identify new potential therapeutic targets. The initiative will deposit all data in a repository that will be accessible for use by the biomedical community. The five year endeavor, beginning in 2014, will result in several sets of project outcomes. For the biomarkers project, tau imaging and EEG data will be released in year two, as baseline data becomes available. Completed data from the randomized, blinded trials will be added after the end of the five year studies. This will include both imaging data and data from blood and spinal fluid biomarker studies. For the network analysis project, each project will general several network models of late onset AD (LOAD) and identify key drivers of disease pathogensis by the end of year three. Years four and five will be dedicated to validating the novel targets and refining the network models of LOAD, including screening novel compounds or drugs already in use for other conditions that may have the ability to modulate the likely targets.

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Cite this (ADHD-200 Preprocessed Data, RRID:SCR_000576)

URL: http://neurobureau.projects.nitrc.org/ADHD200/Introduction.html

Resource Type: Resource, data set, data or information resource

Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau

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Cite this (ADHD-200 Sample, RRID:SCR_005358)

URL: http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html#

Resource Type: Resource, disease-related portal, data set, topical portal, portal, data or information resource

A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU)

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Cite this (Adult Wistar Rat Atlas, RRID:SCR_006288)

URL: http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Resource Type: Resource, atlas, data or information resource

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

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    AFIDs

Cite this (AFIDs, RRID:SCR_016623)

URL: https://github.com/jclauneuro/afids

Resource Type: Resource, software resource, software application, image processing software, data processing software, software toolkit

Software tool as an open framework for evaluating correspondence between magnetic resonance images of the human brain using fiducial placement.

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Cite this (AgedBrainSYSBIO, RRID:SCR_003825)

URL: http://www.agedbrainsysbio.eu/

Resource Type: Resource, organization portal, portal, consortium, data or information resource

Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application.

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Cite this (Aged Rodent Tissue Arrays, RRID:SCR_007332)

URL: http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Resource Type: Resource, biomaterial analysis service, analysis service resource, service resource, production service resource, material analysis service

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

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Cite this (AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders, RRID:SCR_005336)

URL: http://spot.colorado.edu/~dubin/talks/agnosia.html

Resource Type: Resource, data set, terminological resource, data or information resource

Compilation terms with definitions that describe altered states that are associated with brain injury (e.g., trauma, stroke, tumor) or with developmental deficits. Although the list deals with primarily CNS-associated disorders, in some cases the term does not distinguish between a CNS cause or a peripheral or neuromuscular cause. Terms that are primarily psychiatric diagnoses (e.g., schizophrenia) are not included. AGNOSIA is a general term for a loss of ability to recognize objects, people, sounds, shapes, or smells; that is, the inability to attach appropriate meaning to objective sense-data. It usually is used when the primary sense organ involved is not impaired. APHASIA is a general term relating to a loss of language ability. APRAXIA is a general term for disorders of practice. These conditions are usually caused by brain injury due to trauma, stroke and/or tumor. Many of these terms have two synonymous forms that differ in whether the word starts with a- or with dys- such as alexia and dyslexia. Here the a- form is usually defined and the other is noted as syn:, except when the dys- form is the more common usage. (If you cannot find a term in one of these forms, look for it in the other. All other synonyms are defined in both forms.) Sources: These definitions are paraphrased from definitions in a large number or print and online dictionaries. Thus this list is not meant to be considered my own, but rather is a compilation. Note: When a word appears in italics, that indicates it is defined elsewhere in this list.

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