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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data visualization software, data processing software, data analysis software, software application, software resource, image analysis software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html |
SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-02-14 02:03:19 | 5 | ||||||
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SpectraVis Resource Report Resource Website |
SpectraVis (RRID:SCR_016691) | data visualization software, network analysis software, data processing software, web application, data analysis software, network graph visualization software, software application, software resource | Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity. | functional, brain, conectivity, analyzing, network, time, frequency | Free, Available for download, Freely available | http://ericdeno.com/research/SpectraVis/ | SCR_016691 | 2026-02-14 02:03:05 | 0 | ||||||||||
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JOSA Resource Report Resource Website |
JOSA (RRID:SCR_024756) | data processing software, software application, registration software, software resource, image analysis software | Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas. | joint surface based registration, atlas construction, brain, fMRI, brain structure and function, recognizing mismatch between geometry and function, |
is a plug in for: FreeSurfer is organization facet of: BRAIN Initiative Cell Atlas Network |
DOI:10.48550/arXiv.2311.08544 | Restricted | SCR_024756 | JOint Spherical registration and Atlas building | 2026-02-14 02:08:44 | 0 | ||||||||
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FMRIB's Linear Image Registration Tool Resource Report Resource Website 10+ mentions |
FMRIB's Linear Image Registration Tool (RRID:SCR_024922) | FLIRT | data processing software, software application, registration software, software resource, image analysis software | Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration. | linear, affine, intra, inter, modal, brain, image, registration, brain image registration, | is a plug in for: FSL | Free, Freely available | SCR_024922 | 2026-02-14 02:08:37 | 12 | |||||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software resource, software application | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-02-14 02:09:06 | 2 | ||||||||
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VERBENA Resource Report Resource Website |
VERBENA (RRID:SCR_024919) | software resource, software application | Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain. | Dynamic Susceptibility Contrast, quantification of perfusion, haemodynamic parameters, Dynamic Susceptibility Contrast perfusion MRI, brain | is a plug in for: FSL | Free, Freely available | SCR_024919 | VERBENA:Vascular Model Based Perfusion Quantification for DSC-MRI | 2026-02-14 02:08:58 | 0 | |||||||||
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Luxembourg Centre for Systems Biomedicine Resource Report Resource Website |
Luxembourg Centre for Systems Biomedicine (RRID:SCR_026168) | LCSB | institution | Research institute in Esch-sur-Alzette, Luxembourg to study brain and its diseases. Collaboration between biologists, medical and computer scientists, physicists, engineers as well as mathematicians offers new insights into complex biological mechanisms and disease processes, with the aim of developing new tools for diagnostics, prevention, and therapy. LCSB has established strategic partnerships with scientific partners worldwide and with all major biomedical research units in Luxembourg. Carries out collaborative projects with hospitals and research-oriented companies, accelerating translation of fundamental research results into clinical applications. | study brain and its diseases, diagnostics, prevention, therapy, collaborative projects, brain, | has parent organization: University of Luxembourg; Luxembourg; Luxembourg | SCR_026168 | 2026-02-14 02:09:10 | 0 | ||||||||||
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MarmotGraph Resource Report Resource Website |
MarmotGraph (RRID:SCR_027452) | software resource, software application, knowledge graph | Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology | is related to: EBRAINS Knowledge Graph | Free, Freely available, | SCR_027452 | Management Applications for Rich Metadata ObjecTs Graph | 2026-02-14 02:09:31 | 0 | |||||||||
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University of California at Irvine FIBRE Core Facility Resource Report Resource Website |
University of California at Irvine FIBRE Core Facility (RRID:SCR_027777) | core facility, access service resource, service resource | Facility for Imaging and Brain Research houses 3T Siemens Prisma scanner, mock scanner, and data analysis facilities. Research dedicated MRI scanning facility designed to suit wide range of basic and translational research programs by researchers across the UCI campus and beyond. | ABRF, 3T Siemens Prisma scanner, mock scanner, data analysis, imaging, brain |
is listed by: ABRF CoreMarketplace has parent organization: University of California at Irvine; California; USA |
Open | ABRF_5689 | https://coremarketplace.org/RRID:SCR_027777/?citation=1 | SCR_027777 | UC Irvine FIBRE Core Facility., UCI FIBRE, UCI Facility for Imaging and Brain Research | 2026-02-14 02:09:59 | 0 | |||||||
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NeuroVault Resource Report Resource Website 100+ mentions |
NeuroVault (RRID:SCR_003806) | data repository, storage service resource, service resource | Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies. | neuroimaging, fmri, mri, functional mri assay, pet, brain activation map, brain, statistical map, neuroimaging repository |
uses: NeuroSynth is used by: NIF Data Federation is used by: Integrated Datasets is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford Center for Reproducible Neuroscience |
International Neuroinformatics Coordinating Facility ; Max-Planck-Gesellschaft ; Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig; Germany |
Creative Commons Zero License | nlx_158106, r3d100012842 | http://neurovault.org/api https://doi.org/10.17616/R31NJMEI |
SCR_003806 | NeuroVault - A public repository of unthresholded brain activation maps | 2026-02-14 02:00:36 | 342 | ||||||
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MRC Cognition and Brain Sciences Unit Resource Report Resource Website 10+ mentions |
MRC Cognition and Brain Sciences Unit (RRID:SCR_003818) | CBU | data or information resource, organization portal, portal, department portal | Unit studying human cognition and the brain with about 90 researchers and postgraduate students investigating topics such as attention, emotion, language and memory. They are developing new treatments for depression, improving hearing through cochlear implants, and helping children to overcome memory problems. With a large collection of scientists engaged in both basic and translational research on the mind and brain, the Unit provides an exceptional training and academic environment that benefits postgraduate students and researchers at all levels. A significant part of their research makes use of brain imaging and they have excellent on-site facilities for magnetic resonance imaging (MRI) magnetoencephalography (MEG) and electroencephalography (EEG). They also have clinical facilities at Addenbrooke's Hospital. The Unit has close links both with the hospital and with Cambridge University. | cognition, attention, language, memory, emotion, behavior, neuroimaging, computer modelling, brain, depressive disorder, hearing, cochlear implant, child, clinical, mri, magnetoencephalography, eeg, ear, cochlea |
has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: CBU Imaging Wiki is parent organization of: Kymata Atlas |
MRC | nlx_158118, grid.415036.5, Wikidata: Q5141152, ISNI: 0000 0001 2177 2032 | https://ror.org/055bpw879 | SCR_003818 | Cognition and Brain Sciences Unit | 2026-02-14 02:00:52 | 31 | ||||||
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RFMRI.ORG Resource Report Resource Website 50+ mentions |
RFMRI.ORG (RRID:SCR_004042) | R-fMRI Network | community building portal, portal, discussion, data or information resource, forum, narrative resource | A network for supporting resting-state fMRI (R-fMRI) related studies. It connects R-fMRI researchers (as nodes) by their sharings (as edges). Through the network, ideas, comments, resources, tools, experiences, and data can be shared. Researchers (nodes) with basic neuroscience, methodological, or clinical backgrounds can connect with each other in the network. It also contains a preprint server that allows neuroscientists to share their preprints, comment on each others research and get back valuable information about their experiments from their colleagues. This is based on the arXiv model. Ultimately, the network aims to enhance collaborations among researchers, especially to translate knowledge of basic neuroscience and methodology to clinical applications (bench to bedside). | resting-state fmri, fmri, training material, brain |
is parent organization of: DPARSF is parent organization of: DPABI |
nlx_158470 | SCR_004042 | The R-fMRI Network - RFMRI.ORG, The R-fMRI Network a network for supporting resting-state fMRI related studies, R-fMRI Network, The R-fMRI Network - a network for supporting resting-state fMRI related studies, R-fMRI Network (RFMRI.ORG), The R-fMRI Network (RFMRI.ORG): A network for supporting resting-state fMRI related studies! | 2026-02-14 02:00:54 | 71 | ||||||||
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Stanford University, Center for Interdisciplinary Brain Sciences Research Resource Report Resource Website 1+ mentions |
Stanford University, Center for Interdisciplinary Brain Sciences Research (RRID:SCR_004134) | CIBSR | data or information resource, portal, topical portal | The Center for Interdisciplinary Brain Sciences Research (CIBSR) at the Stanford University School of Medicine is dedicated to research that will improve the lives and well-being of individuals with disorders of the brain and improve knowledge of healthy brain and behavioral development. CIBSR research staff are dedicated to identifying biological and environmental risk factors, understanding disease pathophysiology and developmental outcomes, and developing new treatments for neurodevelopmental, neurogenetic and neuropsychiatric disorders of childhood onset. Our research studies are truly multi/interdisciplinary as they bring together experts from the fields of psychiatry, neurology, psychology, computer science, biostatistics and genetics to explore and seek answers for complex questions related to brain-behavior relationships. Active research at CIBSR includes: * Mutlimodal imaging of the brain utilizing anatomical and functional magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS). * Behavioral, cognitive, and physiological assessment to address questions concerning the influence of biological and environmental factors on outcome. * The development of new biological and cognitive-behavioral treatments. * Development of brain image analysis methods and software. | brain, research, child, young human | has parent organization: Stanford University School of Medicine; California; USA | nif-0000-02075 | http://spnl.stanford.edu/index.html | SCR_004134 | Stanford Center for Interdisciplinary Brain Sciences Research | 2026-02-14 02:00:56 | 3 | |||||||
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CanEuCre Resource Report Resource Website 1+ mentions |
CanEuCre (RRID:SCR_004159) | CanEuCre | biomaterial manufacture, material service resource, service resource, production service resource | Cre expressing mice under the control of promoters with a design focus on the brain. Each promoter is derived from human sequence, but the resulting expression is assessed in the mouse for the activation of a LacZ reporter gene by the Cre activity. Promoters tested as large MaxiPromoters (BACs inserted into the mouse genome) and MiniPromoters (plasmid-based sequences inserted either into the mouse genome or introduced within AAV viruses). The Cre-related project continues from the Pleiades Promoter Project. Here is the list of genes for which icre/ERT2 mice are currently in development: AGTR1, CARTPT, CLDN5, CLVS2, CRH, GABRA6, HTR1A, HTR1B, KCNA4, KDM5C, MKI67, NEUROD6, NKX6-1, NOV, NPY2R, NR2E1, OLIG2, POU4F2, SLITRK6, SOX1, SOX3, SOX9,, SPRY1, VSX2 | brain, cre, promoter, expression, transcription, mouse, human, adeno-associated virus (aav) |
is related to: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders has parent organization: University of British Columbia; British Columbia; Canada |
GenomeBC | nlx_143587 | SCR_004159 | CanEuCre | 2026-02-14 02:00:55 | 2 | |||||||
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UAB Alzheimer's Disease Center Resource Report Resource Website |
UAB Alzheimer's Disease Center (RRID:SCR_004305) | ADC, UAB ADC | biomaterial supply resource, material resource, tissue bank, brain bank | The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study. | brain, alzheimer's disease, mild cognitive impairment, brain donation, clinical research database |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Alabama at Birmingham; Alabama; USA |
Alzheimer's disease, Mild Cognitive Impairment, Aging | NIA 1P50 AG16582 | Researchers interested in Alzheimer's disease may access the clinical research data | nlx_143674 | http://main.uab.edu/adc/ http://www.uab.edu/medicine/neurology/alzheimers-disease-center | SCR_004305 | UAB Alzheimer's Disease Center, University of Alabama at Birmingham Alzheimer's Disease Center | 2026-02-14 02:00:56 | 0 | ||||
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BrainNet Europe Resource Report Resource Website 10+ mentions |
BrainNet Europe (RRID:SCR_004461) | BNE | data or information resource, organization portal, portal, consortium | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Consortium of 19 brain banks across Europe with an aim to harmonize neuropathological diagnostic criteria and develop gold standards for quality, safety and ethics standards for brain banking. BrainNet Europe also contributes to research on rare diseases, such as: Pick''s disease or other rare forms of dementia, as well as to questions after the events in the aging brain. Anyone can be a donor - irrespective of disease of the central nervous system or not, because for research purposes, one does not only need tissue samples from ill donors, but also from healthy ones for comparison. | central nervous system, clinical, brain research, brain tissue, brain, tissue, late adult human, brain bank, gold standard, neuropathological diagnosis, tissue handling, safety, quality control, ethics, post mortem, data sharing, tissue sampling, autopsy, microdissection, diagnosis |
is listed by: One Mind Biospecimen Bank Listing is listed by: Consortia-pedia is related to: Medical University of Vienna Institute of Neurology is related to: Human Brain Tissue Bank has parent organization: Ludwig-Maximilians-University; Munich; Germany is parent organization of: BrainNet Europe Sampling Protocols |
Central nervous system disorder, Normal control, Aging, Neurological disease, Psychiatric disease, Pick''s disease, Dementia | European Union FP6 LSHM-CT-2004-503039 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_45326 | SCR_004461 | BrainNet Europe Consortium | 2026-02-14 02:00:41 | 24 | |||||
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Epilepsy Research Ireland Resource Report Resource Website |
Epilepsy Research Ireland (RRID:SCR_004448) | ERI | portal, data or information resource, funding resource, disease-related portal, topical portal | Epilepsy Research Ireland is a non-profit organization (Charity CHY17527), run by a group of volunteers, who are dedicated to find cure for epilepsy by raising awareness and money for research. We can say cure now with much more confidence than we could even 10 years ago because recent advances in genetics, brain imaging and drug therapy, all hold out the promise of that holy grail the cure. We can also say with confidence that you can be part of that push by participating in this new foundation since we have collaborations with doctors and scientists all over Europe, the US and Australia, all of whom share the same goal. Epilepsy research, conducted by Epilepsy Research Ireland, is essential and will deliver benefits across the board. Research planned and already underway by Epilepsy Research Ireland will help develop and improve clinical skills; it will provide a knowledge base to develop new ways to manage and treat epilepsy; it will help in the evaluation of new medical advances. Ultimately we can improve the quality of care and provide greater understanding, better and more accurate diagnosis and more tailored treatments. Ireland is uniquely well-positioned, given its relatively homogenous population to make the goal, of making real discoveries in epilepsy research that will directly improve the lives of people with epilepsy, a realistic one. | epilepsy, brain | nlx_143739 | http://www.epilepsyresearchireland.org/index.php?id=17 | SCR_004448 | 2026-02-14 02:00:58 | 0 | |||||||||
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Childrens Brain Tumor Foundation Resource Report Resource Website |
Childrens Brain Tumor Foundation (RRID:SCR_004422) | CBTF | institution | Children''s Brain Tumor Foundation, a non-profit organization, was founded in 1988 by dedicated parents, physicians and friends. Our mission is to improve the treatment, quality of life and the long term outlook for children with brain and spinal cord tumors through research, support, education, and advocacy to families and survivors. Knowledge is critical for families to access expert care and ensure quality of life. Our free publication A Resource Guide for Parents of Children with Brain and Spinal Cord Tumors is now in its fourth edition, and is full of practical information to sort out the complexities of medical procedures, interruptions in school and social life, and uncertainty about the future. CBTF co-sponsors conferences for families, survivors and health care professionals, offering the latest information about research, treatments and strategies for living. Only scientific research will identify the causes and lead to effective treatments for brain tumors in children. CBTF funds cutting-edge research by scientists at top academic medical centers. Their discoveries hold the promise of improving the lives of affected children today and discovering the means of prevention for future generations. CBTF has awarded over $5 million in grants for basic and clinical research related to pediatric brain and spinal cord tumors. Also, over $625,000 has been given out in Quality of Life Grants. | brain tumor, child, pediatric, spinal cord tumor, tumor, brain, spinal cord, cancer | grid.428138.4, nlx_143732, Crossref funder ID: 100002017 | https://ror.org/0053krp57 | SCR_004422 | Children's Brain Tumor Foundation | 2026-02-14 02:00:43 | 0 | ||||||||
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neuroVIISAS Resource Report Resource Website 1+ mentions |
neuroVIISAS (RRID:SCR_006010) | neuroVIISAS | data visualization software, data processing software, d visualization software, data analytics software, network graph visualization software, software application, software resource | An open framework for integrative data analysis, visualization and population simulations for the exploration of network dynamics on multiple levels. This generic platform allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. neuroVIISAS provide answers to questions like: # How can we assemble data of tracing studies? (Metastudy) # Is it possible to integrate tracing and brainmapping data? (Data Integration) # How does the network of analyzed tracing studies looks like? (Visualization) # Which graph theoretical properties posses such a network? (Analysis) # Can we perform population simulations of a tracing study based network? (Simulation and higher level data integration) neuroVIISAS can be used to organize mapping and connectivity data of central nervous systems of any species. The rat brain project of neuroVIISAS contains 450237 ipsi- and 175654 contralateral connections. A list of evaluated tracing studies are available. PyNEST script generation does work using WINDOWS OS, however, the script must be transferred to a UNIX OS with installed NEST. The results file of the NEST simulation can be visualized and analyzed by neuroVIISAS on a WINDOWS OS. | platform, simulation, mapping data, connectivity data, central nervous system, tracing, connectivity, java, image modality, pynest, nest, animation, brain, nervous system, brain mapping, neuroimaging, terminology, ontology, connectomics, atlas, population spike analysis, analytics, connectome, 3d visualization, visual analytics, ontology |
is listed by: 3DVC has parent organization: University of Rostock; Mecklenburg-Vorpommern; Germany |
PMID:22350719 | nlx_151398 | http://139.30.176.116/index-Dateien/Page455.htm | SCR_006010 | neuro Visualization Imagemapping Information System for Analysis and Simulation | 2026-02-14 02:01:12 | 8 | ||||||
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Atrophy Simulation Package Resource Report Resource Website 1+ mentions |
Atrophy Simulation Package (RRID:SCR_006046) | Atrophy Simulation | software resource, simulation software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. Software package used to simulate brain images with local growth / atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions. | neuroimaging, brain, topology, atrophy, mri, deformation, image registration, brain modeling, biomedical imaging, volume measurement, model, morphology, tissue atrophy, brain tissue | has parent organization: University of Pennsylvania; Philadelphia; USA | PMID:15250639 PMID:16689268 PMID:16997578 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00265 | SCR_006046 | 2026-02-14 02:01:04 | 1 |
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