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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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FMRLAB Resource Report Resource Website 1+ mentions |
FMRLAB (RRID:SCR_005164) | FMRLAB | software application, software resource, data processing software | A Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessary processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure. Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially independent components of the entire data set from the higher-order statistics of the data themselves. FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux. FMRLAB Features * Graphic user interface * Flexible data importing * Interactive data plotting * Computationally efficient * Defined FMRI data structure * Independent component browser * Smooth, transparent component exporting and spatial normalization process * Interface with other software for further analysis or visualization. * SPM-style component plots (MIP, 2-D slice overlay and 3-D) | fmri, fmr lab, anatomy, brain mapping, data analysis, independent component analysis, neuroimaging, image processing, statistical analysis, data visualization, matlab |
is related to: FreeSurfer has parent organization: Swartz Center for Computational Neuroscience |
NIMH 5RO1MHO61619-03 | nif-0000-00077 | SCR_005164 | 2026-07-26 09:03:59 | 3 | ||||||||
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NeuroSynth Resource Report Resource Website 1000+ mentions |
NeuroSynth (RRID:SCR_006798) | Neurosynth | database, software resource, source code, data or information resource | Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image. | activation foci, magnetic resonance imaging assay, brain, human, fmri, neuroimaging, python, image, functional neuroimaging, FASEB list |
is used by: NeuroVault is used by: NIF Data Federation is listed by: GitHub is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brainspell has parent organization: University of Texas at Austin; Texas; USA |
NIMH R01MH096906 | PMID:21706013 | Neurosynth Automated Coordinate Extraction (ACE) tools under, Open unspecified license, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552, Software is, Free, Copyright and permission notice required | nlx_55906 | http://www.nitrc.org/projects/neurosynth, https://github.com/tyarkoni/neurosynth | SCR_006798 | Neurosynth.org | 2026-07-26 09:04:22 | 1174 | ||||
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Neuroscience and Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics Resource Report Resource Website |
Neuroscience and Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics (RRID:SCR_005609) | Neuroscience and Psychiatry Module 1, Neuroscience and Psychiatry Module, Neuroscience Psychiatry Module | video resource, training material, narrative resource, data or information resource | This is the first in a series of modules on neuroscience and psychiatry. This module explores research on cognitive deficits, a core feature of schizophrenia and the single best predictor of functional outcomes in this disorder for which we currently have no treatments. This module is an example of how translational neuroscience can provide clues for the development of promising novel therapeutics. | neuroscience, psychiatry, neural circuit, therapeutics, schizophrenia |
is related to: Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders has parent organization: NIMH Educational Resources |
NIMH | nlx_146228 | SCR_005609 | Neuroscience and Psychiatry Module 1 - Translating Neural Circuits into Novel Therapeutics, Translating Neural Circuits into Novel Therapeutics, Neuroscience Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics | 2026-07-26 09:04:02 | 0 | |||||||
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Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders Resource Report Resource Website |
Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders (RRID:SCR_008843) | Neuroscience and Psychiatry Module 2, Neuroscience Psychiatry Module 2 | video resource, training material, narrative resource, data or information resource | This is the second in a series of modules on neuroscience and psychiatry. This module describes neuroscience research on animal models of fear that informed human studies of fear/safety, anxiety and anxiety disorders. This model helps shed light on the symptoms of PTSD and lead to the development of a novel treatment that has been successful in research studies for several anxiety disorders. | neuroscience, psychiatry, fear, safety, anxiety, anxiety disorder, human, animal model, post-traumatic stress disorder, treatment |
is related to: Neuroscience and Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics has parent organization: NIMH Educational Resources |
NIMH | nlx_146229 | SCR_008843 | Neuroscience Psychiatry Module 2: Fear/Safety Anxiety Anxiety Disorders, Fear/Safety Anxiety and Anxiety Disorders | 2026-07-26 09:04:40 | 0 | |||||||
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SIMS Resource Report Resource Website 1+ mentions |
SIMS (RRID:SCR_025787) | software application, software resource | Software label transfer tool for single-cell RNA sequencing analysis. Scalable, Interpretable Modeling for Single-cell RNA-seq data classification. | label transfer, single-cell RNA sequencing analysis, single-cell RNA-seq data classification, | Schmidt Futures ; NHGRI 1RM1HG011543; NSF ; NIMH 1U24MH132628; University of California Office of the President ; QualcommInstitute |
PMID:38823397 | Free, Available for download, Freely available | SCR_025787 | scalable, interpretable machine learning for single cell | 2026-07-26 09:08:39 | 2 | ||||||||
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RDoC Resource Report Resource Website 100+ mentions |
RDoC (RRID:SCR_002244) | RDoC | narrative resource, standard specification, data or information resource, knowledge environment | NIMH Strategic Plan developing, for research purposes, new ways of classifying psychopathology based on dimensions of observable behavior and neurobiological measures. In brief, the effort is to define basic dimensions of functioning (such as fear circuitry or working memory) to be studied across multiple units of analysis, from genes to neural circuits to behaviors, cutting across disorders as traditionally defined. The intent is to translate rapid progress in basic neurobiological and behavioral research to an improved integrative understanding of psychopathology and the development of new and/or optimally matched treatments for mental disorders. The various domains of functioning, and their constituent elements, are being defined by an ongoing series of consensus workshops; input from the research community and other interested stakeholders is encouraged. | cognitive system, neural circuit, behavior, cognition, comorbidity, psychiatric diagnosis |
is related to: RDoCdb has parent organization: National Institute of Mental Health |
Mental disease | NIMH | PMID:24016027 PMID:23902986 PMID:22577302 PMID:21198381 PMID:20939653 PMID:20929969 PMID:20595427 |
Free, Freely available | nlx_155557 | SCR_002244 | Research Domain Criteria | 2026-07-27 09:31:25 | 156 | ||||
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Cognitive Paradigm Ontology Resource Report Resource Website 1+ mentions |
Cognitive Paradigm Ontology (RRID:SCR_002235) | CogPO | controlled vocabulary, ontology, data or information resource | Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. | functional neuroimaging, owl, cognition, behavior |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: BioPortal is related to: Human Imaging Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA has parent organization: Mind Research Network |
NIMH 1R01MH084812-01A1 | Free, Freely available | nlx_155537 | http://www.nitrc.org/projects/cogpo | SCR_002235 | 2026-07-27 09:31:28 | 9 | ||||||
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Schizophrenia Research Forum Resource Report Resource Website 10+ mentions |
Schizophrenia Research Forum (RRID:SCR_002899) | SRF | portal, disease-related portal, topical portal, data or information resource | The mission of the SRF is to help in the search for causes, treatments, and understanding of the devastating disease of schizophrenia. Our goal is to foster collaboration among researchers by providing an international online forum where ideas, research news, and data can be presented and discussed. The website is intended to bring together scientists working specifically on schizophrenia, scientists researching related diseases, and basic scientists whose work can shed light on these diseases. In this way, we hope that the Schizophrenia Research Forum will be a catalyst for creative thinking in the quest to understand a deeply complex disease. It is our goal to create and maintain up-to-date content of the highest quality. The website is free of charge to users, independent of industry sponsorship, and open to the public. Though geared toward researchers, we welcome other visitorspeople with mental illnesses, families, the media, and others who need accurate information on research into schizophrenia. We do, however, require that users who wish to post comments and other materials be registered members. All such materials are subject to approval by the editorial team. As a forum, we encourage participation and welcome feedback from the community. | schizophrenia | is parent organization of: Schizophrenia Research Forum: Published Candidate Genes for Schizophrenia | Schizophrenia | NIMH ; Brain and Behavior Research Foundation |
nif-0000-00154 | SCR_002899 | Schziophrenia Research Forum - A Catalyst for Creative Thinking | 2026-07-27 09:31:36 | 15 | ||||||
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NIH Image Resource Report Resource Website 1000+ mentions |
NIH Image (RRID:SCR_003073) | NIH Image | image analysis software, software resource, source code, software application, image processing software, data processing software | Public image processing and analysis program for Macintosh. | image processing application, public image processing software, imagej |
is listed by: SoftCite is related to: ImageJ is related to: BrainImage Software is related to: Object-Image has parent organization: National Institutes of Health has parent organization: National Institute of Mental Health |
NINDS ; NIMH |
Free, download Freely available | nif-0000-30469 | https://imagej.net/nih-image/index.html | SCR_003073 | 2026-07-27 09:31:39 | 4412 | ||||||
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NIH NeuroBioBank Resource Report Resource Website 100+ mentions |
NIH NeuroBioBank (RRID:SCR_003131) | NBB | brain bank, biomaterial supply resource, material resource, tissue bank | National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor. | human post-mortem brain tissue, human brain, brain tissue, tissue, adult, child, brain donation, human post-mortem brain tissue and related biospecimens, |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is listed by: One Mind Biospecimen Bank Listing has parent organization: National Institutes of Health |
Brain disorder, Autism spectrum disorder, Autism, Major Depressive Disorder, Schizophrenia, Multiple Sclerosis, Epilepsy, Traumatic brain injury | NIMH ; NINDS ; NICHD ; NIA ; NIDA |
PMID:29496155 | Free, Freely available | nlx_156783 | SCR_003131 | NeuroBioBank, National Institutes of Health NeuroBioBank | 2026-07-27 09:31:40 | 177 | ||||
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BMAP cDNA Resources Resource Report Resource Website 1+ mentions |
BMAP cDNA Resources (RRID:SCR_002973) | BMAP Resources | resource, service resource, material service resource, topical portal, production service resource, portal, data or information resource, biomaterial manufacture | As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com | brain, spinal cord, retina, gene, cdna, library, est, cluster, clone, nervous system, dbest, database, gene discovery, cdna library, expressed sequence tag, coding sequence, adult |
is related to: Nucleotide database is related to: Open Biosystems has parent organization: BMAP - Brain Molecular Anatomy Project |
NINDS ; NICHD ; NIDDK ; NIDA ; NIMH N01 MH80014 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30154 | SCR_002973 | Brain Molecular Anatomy Project cDNA Resources | 2026-07-27 09:31:38 | 2 | ||||||
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BioImage Suite Resource Report Resource Website 50+ mentions |
BioImage Suite (RRID:SCR_002986) | data visualization software, image analysis software, software resource, software application, image processing software, data processing software | Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM. | Analysis, multimodal, multispecies, neuroimaging, data, DTI, fMRI, processing, visualization, registration, surface, editing, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: 3D Slicer has parent organization: Yale University; Connecticut; USA |
NIBIB R03 EB012969; NIBIB R01 EB006494; NIMH MH114805 |
PMID:21249532 | Free, Available for download, Freely available | nif-0000-30179 | https://sources.debian.org/src/bioimagesuite/, http://www.nitrc.org/projects/bioimagesuite, https://medicine.yale.edu/bioimaging/suite/ | http://bioimagesuite.yale.edu/index.aspx | SCR_002986 | Bioimagesuite Web | 2026-07-27 09:31:38 | 54 | ||||
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Allen Brain Cell Atlas Resource Report Resource Website 10+ mentions |
Allen Brain Cell Atlas (RRID:SCR_024440) | expression atlas, atlas, data or information resource | Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression. | visualizing multimodal single cell data across mammalian brain, explore and analyze multiple whole brain datasets, identify cell types in brain, brain regions defined by gene expression, |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH MH130919 | Free, Freely available | SCR_024440 | Allen Brain Cell (ABC) Atlas, The Allen Brain Cell Atlas, ABC Atlas | 2026-07-27 09:37:08 | 42 | ||||||||
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Functional Regression Analysis of DTI Tract Statistics Resource Report Resource Website |
Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) | FRATS | software application, image analysis software, software resource, data processing software | Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. | computational neuroscience, imaging genomics, magnetic resonance, regression analysis, dti, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NSF BCS-08-26844; NCRR UL1-RR025747-01; NIMH MH086633; NIA AG033387; NIMH MH064065; NICHD HD053000; NIMH MH070890; NINDS R01NS055754; NIBIB U54 EB005149-01 |
PMID:20335089 | Academic Free License | nlx_155629 | SCR_002293 | Functional Regression Analysis of DTI | 2026-07-27 09:31:30 | 0 | |||||
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Common Cell Type Nomenclature Resource Report Resource Website 1+ mentions |
Common Cell Type Nomenclature (RRID:SCR_021124) | controlled vocabulary, narrative resource, data or information resource, standard specification | Framework for creating brain cell type nomenclature, and include examples using published datasets. System allows designation of cell types with or without hierarchical organization. Nomenclature convention initially applied to brain cells and types, is intended to encompass existing naming strategies used in publications across diverse research teams. Allows tracking of many different taxonomies, including those from different organ systems or across diverse areas of bioscience. | Allen Cell Type Nomenclature CCN, Allen Brain Map, Common Cell Type Nomenclature, CCN, creating brain cell type nomenclature, hierarchical organization, nomenclature convention, naming strategies, taxonomies tracking |
is related to: Allen Brain Atlas is related to: Brain Data Standards Ontology is related to: Cell Type Knowledge Explorer has parent organization: Allen Institute |
Allen Institute ; NIMH U19 MH114830; NIMH U01 MH114812 |
PMID:33372656 | Free, Available for download, Freely available | https://github.com/AllenInstitute/nomenclature, https://github.com/AllenInstitute/CCN | SCR_021124 | Allen Cell Type Common Cell type Nomenclature, Allen Brain Map Cell Type Nomenclature CCN | 2026-07-27 09:36:16 | 3 | ||||||
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ARGON Resource Report Resource Website 1+ mentions |
ARGON (RRID:SCR_021635) | software application, simulation software, software resource | Software tool as fast simulator of genetic data that samples from Discrete Time Wright Fisher process backwards in time. Used to simulate long chromosomes and large samples under DTWF, with computational time comparable to recent coalescent simulators. | DTWF, genetic data simulator, discrete time Wright Fisher, process backwards in time, large samples simulation, long chromosomes simulation, discrete time Wright Fisher, coalescent simulation | has parent organization: University of Oxford; Oxford; United Kingdom | NIMH R01 MH101244 | PMID:27312410 | Free, Available for download, Freely available | https://github.com/pierpal/ARGON | SCR_021635 | 2026-07-27 09:36:24 | 1 | |||||||
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FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | data visualization software, data analysis software, software resource, software application, data processing software | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: University of California at Berkeley; Berkeley; USA |
National Institutes of Health NRSA Trainee appointment ; California Research Alliance by BASF ; NIMH U01 MH105979; NHGRI U01 HG007910 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-07-27 09:35:30 | 0 | ||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | data visualization software, data analysis software, software resource, software application, data processing software | Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data. | Executing, evaluating, visualizing, clustering, experimental, data, single, cell, RNAseq, sequencing, gene, expression, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH U19 MH114830; NIMH U01 MH105979; Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-07-27 09:35:30 | 0 | ||||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | image analysis software, software resource, software application, image processing software, data processing software | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIDA DA018310; NIMH U01 MH109062; National Science Foundation Graduate Research Fellowship Program ; Springborn Fellowship ; NIGMS T32 GM070421 |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-07-27 09:35:30 | 1 | |||||||
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StimVision Resource Report Resource Website 1+ mentions |
StimVision (RRID:SCR_017457) | software application, data visualization software, data processing software, software resource | Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room. | Tractography, deep, brain, stimulation, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH R01 MH102238; NIMH R01 MH106173 |
PMID:28653482 | SCR_017457 | Stim Vision, StimVision | 2026-07-27 09:35:40 | 1 |
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