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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, atlas, data analysis service, data or information resource, data repository, database, image repository, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-09-05 06:24:53 | 14 | ||||
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Stanley Neuropathology Consortium Integrative Database Resource Report Resource Website 10+ mentions |
Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) | SNCID | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service resource | A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access. | schizophrenia, bipolar disorder, depressive disorder, brain, blinded study, microarray, single-nucleotide polymorphism, mental disorder, biomarker | has parent organization: Stanley Medical Research Institute | Schizophrenia, Bipolar Disorder, Depressive Disorder, Mental disorder | PMID:19829293 | Free | nif-0000-24103 | SCR_002749 | Stanley Neuropathology Consortium Integrative Database | 2026-09-05 06:24:53 | 20 | |||||
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NIH Office of Science Education Resource Report Resource Website |
NIH Office of Science Education (RRID:SCR_005603) | OSE | data or information resource, knowledge environment, narrative resource, organization portal, portal, training material | The NIH Office of Science Education (OSE) coordinates science education activities at the NIH and develops and sponsors science education projects in house. These programs serve elementary, secondary, and college students and teachers and the public. Activities * Develop curriculum supplements and other educational materials related to medicine and research through collaborations with scientific experts at NIH * Maintain a website as a central source of information about NIH science education resources * Establish national model programs in public science education, such as the NIH Mini-Med School and Science in the Cinema * Promote science education reform as outlined in the National Science Education Standards and related guidelines The OSE was established in 1991 within the Office of Science Policy of the Office of the Director of the National Institutes of Health. The NIH is the world''s foremost biomedical research center and the U.S. federal government''s focal point for such research. It is one of the components of the Department of Health and Human Services (HHS). The Office of Science Education (OSE) plans, develops, and coordinates a comprehensive science education program to strengthen and enhance efforts of the NIH to attract young people to biomedical and behavioral science careers and to improve science literacy in both adults and children. The function of the Office is as follows: (1) develops, supports, and directs new program initiatives at all levels with special emphasis on targeting students in grades kindergarten to 16, their educators and parents, and the general public; (2) advises NIH leadership on science education issues; (3) examines and evaluates research and emerging trends in science education and literacy for policy making; (4) works closely with the NIH extramural, intramural, women''s health, laboratory animal research, and minority program offices on science education special issues and programs to ensure coordination of NIH efforts; (5) works with NIH institutes, centers, and divisions to enhance communication of science education activities; and (6) works cooperatively with other public- and private-sector organizations to develop and coordinate activities. | science, education, high school, middle school, elementary school, animal, research, bioethics, blood, lymphatic system, bones, joints, muscle, brain, nervous system, cell biology, cancer, child, adolescent, complementary medicine, alternative medicine, digestive system, ears, nose, throat, endocrine system, environmental, toxicology, evolution, eye, vision, food, nutrition, metabolism, genomics, genetics, heart, circulation, history, immune system, injury, wound, kidney, urinary system, medical research, man, mental health, behavior, microbiology, infectious disease, mouth, teeth, therapy, reproductive system, respiratory system, safety, late adult human, sexual health, skin, hair, nail, sleep, social, family, substance abuse, technology, wellness, lifestyle, woman, health, human, lesson plan, supplemental curricula, book, image, multimedia, poster, k-12, adult, non-human animal |
has parent organization: National Institutes of Health is parent organization of: NIH SciEd Blog |
NIH | nlx_146222 | SCR_005603 | NIH OSE, National Institutes of Health Office of Science Education | 2026-09-05 06:25:38 | 0 | |||||||
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Brain Basics Resource Report Resource Website |
Brain Basics (RRID:SCR_005606) | Brain Basics | data or information resource, narrative resource, training material, video resource | Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression. | brain, depression, anxiety disorder, bipolar disorder, attention deficit-hyperactivity disorder, depressive disorder, mental disease, gene, environment | has parent organization: NIMH Educational Resources | NIMH | nlx_146226 | SCR_005606 | NIMH Brain Basics | 2026-09-05 06:25:38 | 0 | |||||||
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BrainStars Resource Report Resource Website 10+ mentions |
BrainStars (RRID:SCR_005810) | B* | data access protocol, data or information resource, database, software resource, web service | BrainStars (or B*) is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions. For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope. For each region, we took samples every 4 hours, starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24 hours (6 time-point samples for each region), and we pooled the samples from the different time points. We independently sampled each region twice (n=2). These samples were purified their RNA, and measured with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Expression values were then summarized with the RMA method. After several analysis with the expression data, the data and analysis results were stored in the BrainStars database. The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API. | mouse, brain, adult, expression profile, affymetrix genechip mouse genome 430 2.0 array, rna, central nervous system, gene expression, gene |
is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science has parent organization: RIKEN has parent organization: Kindai University School of Medicine; Osaka; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21858037 | BrainStars data, Images and texts (excluding ABA data and images) are licensed under a Creative Commons Attribution 2.1 Japan License. | nlx_149301 | SCR_005810 | BrainStars Database, BrainStars (B*) | 2026-09-05 06:25:42 | 15 | |||||
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ViBE-Z Resource Report Resource Website 1+ mentions |
ViBE-Z (RRID:SCR_005895) | ViBE-Z | atlas, data or information resource, data processing software, database, image processing software, software application, software resource | An imaging and image analysis framework for virtual colocalization studies in larval zebrafish brains, currently available for 72hpf, 48hpf and 96hpf old larvae. ViBE-Z contains a database with precisely aligned gene expression patterns (1����m^3 resolution), an anatomical atlas, and a software. This software creates high-quality data sets by fusing multiple confocal microscopic image stacks, and aligns these data sets to the standard larva. The ViBE-Z database and atlas are stored in HDF5 file format. They are freely available for download. ViBE-Z provides a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. ViBE-Z enhances the data quality through fusion and attenuation correction of multiple confocal microscope stacks per specimen and uses a fluorescent stain of cell nuclei for image registration. It automatically detects 14 predefined anatomical landmarks for aligning new data with the reference brain. ViBE-Z performs colocalization analysis in expression databases for anatomical domains or subdomains defined by any specific pattern. The ViBE-Z database, atlas and software are provided via a web interface. | brain, larval zebrafish, gene expression, confocal microscopy | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | Excellence Initiative of the German Federal and State Governments ; European Union |
PMID:22706672 | nlx_149465 | SCR_005895 | Virtual Brain Explorer for Zebrafish, Virtual Brain Explorer, ViBE-Z: The Virtual Brain Explorer for Zebrafish | 2026-09-05 06:25:43 | 4 | ||||||
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Expression Atlas of the Marmoset Resource Report Resource Website 1+ mentions |
Expression Atlas of the Marmoset (RRID:SCR_005760) | Marmoset Expression Atlas, RIKEN Marmoset Expression Atlas | atlas, data or information resource, data set, expression atlas | Database of gene expression in the marmoset brain.Comparative anatomy of marmoset and mouse cortex from genomic expression. Atlas comparing brain of neonatal marmoset with mouse using in situ hybridization. | gene, marmoset, gene expression, neonatal, brain, in situ hybridization, gene, cortex, thalamus, dorsal nucleus of lateral geniculate body, dlgn, subplate, hippocampus, primary somatosensory cortex, btbd3, cdh6, cdh8, cplx3, ctgf, epha4, epha5, epha6, epha7, efna5, er81, foxp2, gfralpha1, kitl, lhx9, nr1d1, nr4a2, ntng2, relin, roralpha, satb2, sema6a, tbr1, tcf7l2, zic1, zic4, genomic expression |
is used by: NIF Data Federation has parent organization: RIKEN Brain Science Institute |
RIKEN Brain Science Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Funding Program for World-Leading Innovative RD on Science and Technology |
PMID:22496550 | nlx_149225 | http://mmtd.brain.riken.jp/P0marmoset/ | SCR_005760 | Marmoset Gene List, Comparative Anatomy of Marmoset and Mouse Cortex from Genomic Expression, Comparative Anatomy of Marmoset Mouse Cortex from Genomic Expression | 2026-09-05 06:25:41 | 5 | |||||
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North Texas Traumatic Brain Injury Model System Resource Report Resource Website |
North Texas Traumatic Brain Injury Model System (RRID:SCR_005879) | NT-TBIMS | data or information resource, portal, topical portal | The 16 affiliated Model System centers throughout the United States are responsible for gathering and submitting the core data set to the national database as well as conducting research studies on traumatic brain injury (TBI) both in collaboration with the other centers and within our own site. Through our research we hope to learn more about TBI and about the issues and concerns of people with TBI. Our goals are to improve the outcome and quality of life for people who have had brain injuries and for those who are caring for the person with a TBI. The North Texas Traumatic Brain Injury Model System (NT-TBIMS) pools the efforts and talents of individuals from the Departments of Neurosurgery, Neurology, Physical Medicine and Rehabilitation, Psychiatry (Neuropsychiatry), and Neuroradiology of the two leading medical institutions in the North Texas region. To be a patient involved in the research being conducted by the North Texas Traumatic Brain Injury Model System you must have suffered a TBI, be at least 16 years of age, have received initial treatment for the TBI at either Parkland Health and Hospital System or Baylor University Medical Center and then have received rehabilitative care at either Parkland, University Hospital Zale-Lipshy, or Baylor Institute for Rehabilitation. The patient must also be able to understand and sign an informed consent to participate or, if unable, have a family member or a legal guardian who understands the form sign the informed consent for the patient. | brain injury, brain, injury, traumatic brain injury, clinical, research | has parent organization: University of Texas Southwestern Medical Center; Texas; USA | Traumatic Brain Injury | National Institute on Disability and Rehabilitation Research H133A070027 | nlx_149440 | SCR_005879 | North Texas TBI Model System, North Texas Traumatic Brain Injury Model System (NT-TBIMS) | 2026-09-05 06:25:43 | 0 | ||||||
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Brains Matter Resource Report Resource Website |
Brains Matter (RRID:SCR_005847) | Brains Matter | data or information resource, narrative resource, podcast | Welcome to the Brains Matter podcast where brains really do matter. A discussion of science, trivia, history, and general knowledge. The show started in September 2006, and includes discussion on various topics, as well as interviews with experts in their field. You can subscribe to the show via iTunes, a standard RSS reader, or listen to the individual MP3 shows from the ''flash player'' on the website, or direct download. | brain, science | Copyright under the Creative Commons licence where appropriate, Except where otherwise specified. | nlx_149376 | SCR_005847 | Brains Matter - The Podcast on Science Curiosities and General Knowledge. Brains Really Do Matter! | 2026-09-05 06:25:42 | 0 | ||||||||
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Brain Networks Resource Report Resource Website 1+ mentions |
Brain Networks (RRID:SCR_005841) | Brain Networks | data analysis software, data processing software, software application, software resource, source code | Brain Networks: Code to perform network analysis on brain imaging data. | brain, imaging, network analysis, brain imaging, neuroimaging | has parent organization: SourceForge | PMID:21031030 | Open unspecified license - GNU General Public License (GPL) | nlx_149364 | SCR_005841 | brainnetworks | 2026-09-05 06:25:42 | 1 | ||||||
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MIALAB - Medical Image Analysis Lab Resource Report Resource Website 10+ mentions |
MIALAB - Medical Image Analysis Lab (RRID:SCR_006089) | MIALAB | data or information resource, laboratory portal, organization portal, portal | MIALAB, headed by Dr. Vince Calhoun, focuses on developing and optimizing methods and software for quantitative analysis of structure and function in medical images with particular focus on the study of psychiatric illness. We work with many types of data, including functional magnetic resonance imaging (fMRI), diffusion tensor imaging (DTI), electroencephalography (EEG), structural imaging and genetic data. Much of our time is spent working on new methods for flexible analysis of brain imaging data. The use of data driven approaches is very useful for extracting potentially unpredictable patterns within these data. However such methods can be further improved by incorporating additional prior information as constraints, in order to benefit from what we know. To this end, we draw heavily from the areas of image processing, adaptive signal processing, estimation theory, neural networks, statistical signal processing, and pattern recognition. | software, data, data visualization, medical image, image, neuroimaging, fmri, diffusion tensor imaging, electroencephalography, structural imaging, genetic data, brain, image processing, adaptive signal processing, estimation theory, neural network, statistical signal processing, pattern recognition, mri |
has parent organization: Mind Research Network is parent organization of: Group ICA of fMRI Toolbox is parent organization of: Group ICA Of EEG Toolbox is parent organization of: MIALAB - Resting State Data |
Mental disease | nlx_151551 | SCR_006089 | Medical Image Analysis Lab, Medical Image Analysis Laboratory, MIA Laboratory, Medical Image Analysis (MIA) Laboratory | 2026-09-05 06:25:47 | 27 | |||||||
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Allen Brain Atlas API Resource Report Resource Website 10+ mentions |
Allen Brain Atlas API (RRID:SCR_005984) | Allen Brain Atlas API | data or information resource, portal, software application, software resource, source code, topical portal | API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service | atlas application, expression data, 3d volume, 3d coordinate, gene, reference atlas, connectivity, histology, microarray, brain, rna sequencing, mri, dti, api, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics, ish, high resolution image, nissl, annotation, atlas, image, web service, neuroblast, gene expression, gene, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Mouse Brain Reference Atlas is related to: Allen Developing Mouse Brain Atlas is related to: International Neuroinformatics Coordinating Facility is related to: Brain Explorer Atlas and Teaching Tool is related to: CellTax vignette is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science |
Other/Commercial license License | nlx_151358 | http://www.nitrc.org/projects/incf_allen-brai | SCR_005984 | 2026-09-05 06:25:45 | 13 | |||||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | collaboration tool, data management software, data processing software, software application, software resource | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-09-05 06:25:45 | 16 | |||||
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ABC (Atlas Based Classification) Resource Report Resource Website 1+ mentions |
ABC (Atlas Based Classification) (RRID:SCR_005981) | ABC | data processing software, image analysis software, software application, software resource, workflow software | 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. | brain, image, image registration, filter, segmentation, inhomogeneity correction, beta, c++, linux, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of Utah; Utah; USA |
3D Slicer License | nlx_151362 | SCR_005981 | 2026-09-05 06:25:45 | 3 | ||||||||
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Computerized Anatomical Reconstruction and Editing Toolkit Resource Report Resource Website 50+ mentions |
Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) | CARET | data processing software, data visualization software, image processing software, software application, software resource | Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems. | reconstruction, visualization, cerebral cortex, surface, brain, dataset, cerebellar cortex, atlas application, mesh generation, quantitative shape analysis, segmentation, shape analysis, intersubject, image-to-template, gaussian curvature, mean curvature, animation, three dimensional display, two dimensional display, surface rendering, cortical flat map, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SumsDB has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NEI EY02091; NIMH R01 MH60974 |
PMID:11522765 | Free, Available for download, Freely available | nif-0000-00279 | http://www.nitrc.org/projects/caret, https://sources.debian.org/src/caret/ | SCR_006260 | Computerized Anatomical Reconstruction Editing Toolkit | 2026-09-05 06:25:49 | 59 | ||||
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Mind Research Network Resource Report Resource Website 10+ mentions |
Mind Research Network (RRID:SCR_002925) | MRN | nonprofit organization | Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility. | imaging, neuroimaging, magnetic resonance imaging, magnetoencephalogram, brain, forensics, medical image analysis, neurodevelopment, neuroinformatics, data sharing, clinical, cognitive, service resource, instrument manufacture, imaging technology, neuroscience, genetics |
has parent organization: University of New Mexico; New Mexico; USA is parent organization of: Mind Research Network - COINS is parent organization of: MEGSIM is parent organization of: MIALAB - Medical Image Analysis Lab is parent organization of: COBRE is parent organization of: Cognitive Paradigm Ontology |
Mental illness, Brain injury, Traumatic brain injury, Addiction, Autism, Psychosis, Behavioral disorder | nif-0000-00474, grid.280503.c, Wikidata: Q7751519, ISNI: 0000 0004 0409 4614 | https://ror.org/032cjfs80 | SCR_002925 | Mind Research Network for Neuroscience Discovery | 2026-09-05 06:24:55 | 10 | ||||||
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FSL Resource Report Resource Website 5000+ mentions |
FSL (RRID:SCR_002823) | software library, software resource, software toolkit | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
BBSRC ; EPSRC ; GlaxoSmithKline ; MRC ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, SCR_007368, birnlex_2067 | http://www.nitrc.org/projects/fsl, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/, https://sources.debian.org/src/fsl/ | SCR_002823 | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-09-05 06:24:54 | 5015 | |||||
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studyforrest.org Resource Report Resource Website 10+ mentions |
studyforrest.org (RRID:SCR_003112) | studyforrest.org | data repository, image repository, service resource, storage service resource | An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data. | neuroimaging, open data, brain, brain scan, fmri, stimulus material, participant demographic, stimulus, demographic, experimental protocol, structure mri, mri, 7-tesla, data set, auditory system, language, perception |
uses: OpenNeuro uses: rsync uses: XNAT - The Extensible Neuroimaging Archive Toolkit is used by: NIF Data Federation is listed by: NITRC-IR is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
BMBF 01GQ1112; BMBF 01GQ1411; NSF 1129855; DFG PO 548/15-1 |
Free, Available for download, Freely available | r3d100011071, nlx_156710 | http://www.nitrc.org/projects/studyforrest, https://doi.org/10.17616/R3SW5S | SCR_003112 | study forrest, studyforrest | 2026-09-05 06:24:58 | 36 | |||||
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flytrap Resource Report Resource Website 10+ mentions |
flytrap (RRID:SCR_003075) | Flytrap | data or information resource, database, image, video resource | Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use. | brain, genetics, 3d model, expression pattern, anatomy, anatomical structure, cell, gene expression, brain function, neuroimaging, FASEB list | has parent organization: University of Edinburgh; Scotland; United Kingdom | BBSRC ; EPSRC |
PMID:14681446 | Free, Freely available | nif-0000-00051, r3d100011203 | https://doi.org/10.17616/R3VD0P | SCR_003075 | 2026-09-05 06:24:57 | 48 | |||||
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brainmap.org Resource Report Resource Website 100+ mentions |
brainmap.org (RRID:SCR_003069) | BrainMap | data or information resource, database, software application, software resource | A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results | 3d model, atlas, data management, imaging, map, neuroinformatics, warping, neuroimaging, brain, talairach, mni, java, modeling, magnetic resonance, nifti-1, ontology, os independent, pet, spect, visualization, functional neuroimaging, fmri |
uses: Scribe is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brede Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA is parent organization of: Sleuth is parent organization of: GingerALE |
Healthy, Diseased | NIMH 2R01-MH074457 | PMID:15897617 PMID:11967563 PMID:15846810 |
Free, Freely available | nif-0000-00049 | http://www.nitrc.org/projects/brainmap | SCR_003069 | BrainMap Database | 2026-09-05 06:24:57 | 484 |
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