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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Primate Data Exchange Resource Report Resource Website 10+ mentions |
Primate Data Exchange (RRID:SCR_016435) | PRIME-DE | database, organization portal, portal, consortium, data or information resource | Open resource for nonhuman primate imaging.Used for aggregation independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI).Consortium and data collection for the neuroimaging community to map the non-human primate connectome. Anatomical, functional, and diffusion MRI datasets openly shared via the International Neuroimaging Data sharing Initiative (INDI). | nonhuman, primate, neuroimaging, magnetic, resonance, imaging, dataset, share | is affiliated with: 1000 Functional Connectomes Project | the BRAIN Initiative ; the Sylvio O. Conte Center “Neurobiology and Dynamics of Active Sensing” ; the Max Planck Society ; Joseph P. Healy ; NIMH R01 MH111439; NIMH P50 MH109429 |
DOI:10.1016/j.neuron.2018.08.039 | Restricted | SCR_016621 | SCR_016435 | PRIME-DE:PRIMate Data Exchange | 2026-07-27 09:35:17 | 12 | |||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | software application, software resource, data processing software, data analysis software | Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI K12 CA139160; NCI F32CA165823; NIMH T32 MH020065; NIMH R01 MH101820; NIMH R01 MH090937; NIGMS U01 GM61393; NIMH P50 MH094267; NIGMS U01 GM092691; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-07-27 09:35:24 | 23 | |||||||||
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seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | software application, software resource, data processing software, data analysis software | Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers. | sequence, structure, high, dimention, dataset, neuroscience, repeated, sequential, pattern, data | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Simons Foundation Simons Collaboration for the Global Brain ; NIDCD R01 DC009183; G Harold and Leila Y. Mathers Foundation ; U.S. Department of Defense NDSEG Fellowship program ; Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; NIBIB T32 EB019940; NINDS U19 NS10 4648; NIMH R25 MH062204 |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-07-27 09:35:29 | 5 | ||||||||
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PAGODA Resource Report Resource Website |
PAGODA (RRID:SCR_017099) | software application, software resource, data processing software, data analysis software | Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells. | heterogeneity, transcriptional, detect, statistically, cell, classified, overlapping, gene, set, coordinated, variability |
is related to: pagoda2 has parent organization: Harvard University; Cambridge; United States |
Ellison Medical Foundation ; NSF NSF-14-532; NSF DGE1144152; NIMH U01 MH098977; NINDS R01 NS084398; NIA T32 AG00216 |
PMID:26780092 | Free, Available for download, Freely available | http://hms-dbmi.github.io/scde/index.html | SCR_017099 | Pathway And Gene set OverDispersion Analysis, pagoda | 2026-07-27 09:35:25 | 0 | ||||||
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Analysis of Functional NeuroImages Resource Report Resource Website 1000+ mentions |
Analysis of Functional NeuroImages (RRID:SCR_005927) | AFNI | data visualization software, data analysis software, software resource, source code, software application, data processing software, software toolkit | Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries. | c program, unix, fmri, solaris, nifti-1 support, 2d surface analysis, 3d surface analysis, visualization |
uses: Neuroimaging Data Model is used by: 3dsvm is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: BASH4RfMRI has parent organization: National Institute of Mental Health is parent organization of: Mapping Data to the Talairach Atlas works with: NIAG Addiction Data |
NIMH | Free, Open Source, Runs on Linux, Runs on Mac OS | nif-0000-00259 | http://www.nitrc.org/projects/afni | SCR_005927 | AFNI NIfTI Server, AFNI and NIfTI Server | 2026-07-27 09:32:24 | 2107 | |||||
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Brain Test Resource Report Resource Website |
Brain Test (RRID:SCR_006212) | Brain Test | portal, topical portal, data or information resource | A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help. | neuropsychiatry, brain, behavior, behavioral assessment, questionnaire, cognitive test, crowdsourcing, online study, memory, attention, brain disease, gene, exercise, genetics, mental disease, mental health, research project, research | has parent organization: University of California at Los Angeles; California; USA | Attention deficit-hyperactivity disorder, Schizophrenia, Bipolar Disorder, Mental disease, Normal, Autism Spectrum Disorder | NIMH ; NARSAD |
nlx_151777 | SCR_006212 | Brain Test project | 2026-07-27 09:32:29 | 0 | ||||||
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Genes Cognition and Psychosis Program Resource Report Resource Website 1+ mentions |
Genes Cognition and Psychosis Program (RRID:SCR_006292) | GCAP | portal, disease-related portal, topical portal, data or information resource | Schizophrenia related portal that aims to solve the mystery of genetic predisposition to psychosis, develop new methods for early diagnosis and prevention, and discover new treatments that will cure people suffering from it. Our objectives are to fully characterize: # neurobiological mechanisms related to susceptibility genes for schizophrenia and related clinical disorders; # genetic variation in aspects of cognition and emotionality associated with schizophrenia; and # small molecular targets for novel therapies. A unique feature of this Program is that its diverse scientific resources will be focused on a highly specific scientific agenda, that is to acquire the critical biological information about the susceptibility genes associated with schizophrenia and related illnesses. Our mission and goal, to understand the basic mechanisms of serious mental illness, has again guided us into new areas of research and to new insights. We have found evidence of new genes implicated in the cause of schizophrenia and involved in brain functions related to cognition and emotion and we have begun to explore how genes interact with each other and with the environment to individualize risk for these conditions. We are working now with over 20 genes related to schizophrenia. One of the key developments in our research over the past year has been the emergence of some targets for the development of novel therapeutics. We have discovered a new schizophrenia susceptibility gene, KCNH2, which represents the first clear target for the development of novel treatments. Just in this past year, for example, we published the first extensive statistical analysis of how schizophrenia genes may vary in their risk effects based on different genetic background (Nicodemus et al Hum Gen 2006), the first studies of schizophrenia genes interacting in effecting gene expression in brain (Lipska et al Hum Mol Genetics 2006a, Lipska et al Hum Mol Gen 2006 b); the first evidence that the mechanism of genetic association of NRG1 with schizophrenia involves a novel isoform of the gene in human brain (Law et al PNAS 2006), and the first evidence that MAOA may be linked to mood and impulse control because it effects critical mood regulatory neural networks (Meyer-Lindenberg et al PNAS 2006). | gene, genetic variation, cognition, emotion, therapeutics, treatment, drug development, brain function, psychosis, drug |
is related to: NIMH Intramural Research Program Clinical Brain Disorders Branch has parent organization: NIMH Division of Intramural Research Programs |
Schizophrenia, Mental illness, Psychiatric disorder | NIMH | nlx_151948 | SCR_006292 | 2026-07-27 09:32:30 | 1 | |||||||
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HUDSEN Human Gene Expression Spatial Database Resource Report Resource Website |
HUDSEN Human Gene Expression Spatial Database (RRID:SCR_006325) | HUDSEN Database | atlas, service resource, database, storage service resource, data repository, data or information resource | Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ''''anatomical tree''''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development. | embryonic human, anatomy, developmental stage, development, brain, gene expression, optical projection tomography, carnegie stage, in situ hybridization, immunohistochemistry, gene, ontology, anatomical structure, protein expression, embryonic development, annotation, embryo |
is related to: EMAGE Gene Expression Database is related to: Human Developmental Biology Resource has parent organization: HUDSEN |
NIMH 5RO1MH070370; EU FP6 Research Infrastructure Action Structuring the European Research Area Programme contract 011993; Spanish Ministry of Science and Innovation BFU2008-04156; SENECA Foundation contract 04548 �GERM �06-10891 |
PMID:20979583 | Open unspecified license, Acknowledgement requested | nlx_152026 | SCR_006325 | HUDSEN Gene Expression Database | 2026-07-27 09:32:31 | 0 | |||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | data visualization software, image analysis software, software resource, software application, data processing software | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-07-27 09:32:36 | 93 | |||||
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MITRE Neuroinformatics Resource Report Resource Website |
MITRE Neuroinformatics (RRID:SCR_006508) | MITRE Neuroinfomatics | data visualization software, data analysis software, simulation software, software resource, software application, data distribution software, data processing software, data transfer software | This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality. | brain, data, diffusion tensor image, distorted, human, imagery, image, informatics, investigator, laboratory, magnetic resonance image, mapping, neuroscience, structural, visualization, neuroimaging | Human Brain Project ; MITRE Technology Program ; NSF ; NIMH R01-MH64417 |
nif-0000-10469 | http://neuroinformatics.mitre.org/ | SCR_006508 | Neuroinfomatics at MITRE, Neuroinformatics: Exploring the Human Brain | 2026-07-27 09:32:34 | 0 | |||||||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | service resource, database, standard specification, catalog, data set, narrative resource, data or information resource | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NHGRI U01 HG004597; NHGRI U41HG007050; NIDA ; OBSSR ; NIMH ; NHLBI ; NIMHD ; TRSP ; NHGRI U24 HG012556; ODP ; NINDS ; NCI |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-07-27 09:32:34 | 61 | ||||
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Functional Connectivity Toolbox Resource Report Resource Website 100+ mentions |
Functional Connectivity Toolbox (RRID:SCR_006394) | Functional Connectivity Toolbox | data analysis software, software resource, software application, data processing software, software toolkit | MATLAB toolbox for performing functional connectivity analyses includes many of the most commonly-used approaches researchers have utilized to date for the identification of condition-dependent functional interactions between fMRI time-series obtained from two or more brain regions. The approaches are either bivariate or multivariate methods defined in time or frequency domains that emphasize distinct features of relationships among the time-series. | functional connectivity, fmri, matlab, brain region, brain, function, connectivity, neuroimaging, time-series | has parent organization: University of Pittsburgh; Pennsylvania; USA | NIMH K25 MH076981-01; NSF DMS-0904825; NIMH MH074807; NIMH MH082998 |
PMID:19520177 | Free | nlx_152228 | SCR_006394 | 2026-07-27 09:32:32 | 239 | ||||||
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NIMH Division of Intramural Research Programs Resource Report Resource Website 1+ mentions |
NIMH Division of Intramural Research Programs (RRID:SCR_006860) | DIRP | training resource, organization portal, postdoctoral program resource, portal, data or information resource | The Division of Intramural Research Programs (DIRP) at the National Institute of Mental Health (NIMH) is the internal research division of the NIMH. NIMH DIRP scientists conduct research ranging from studies into mechanisms of normal brain function, conducted at the behavioral, systems, cellular, and molecular levels, to clinical investigations into the diagnosis, treatment and prevention of mental illness. Major disease entities studied throughout the lifespan include mood disorders and anxiety, schizophrenia, obsessive-compulsive disorder, attention deficit hyperactivity disorder, and pediatric autoimmune neuropsychiatric disorders. Because of its outstanding resources, unique funding mechanisms, and location in the nation''s capital, the DIRP is viewed as a national resource, providing unique opportunities in mental health research and research training. Training is conducted in all the Institute''s clinical branches and basic neuroscience laboratories located on the 305-acre National Institutes of Health campus in Bethesda, Maryland. In addition to individualized trainee/mentor-driven postdoctoral training opportunities in the clinical and basic sciences, the DIRP offers Postbaccalaureate Research Training Awards, a Clinical Electives Program, as well as a variety of Summer Research Fellowships and an Undergraduate Internship Program. The mission of the division is to plan and conduct basic, clinical, and translational research to advance understanding of the diagnosis, causes, treatment, and prevention of mental disorders through the study of brain function and behavior; conduct state-of-the-art research that, in part, complements extramural research activities and exploits the special resources of the National Institutes of Health; and provide an environment conducive to the training and development of clinical and basic scientists. In addition the DIRP fosters standards of excellence in the ethical treatment and the provision of clinical care to research subjects; serve as a resource to the NIMH in responding to requests made by the Administration, members of Congress, and citizens'' groups for information regarding mental disorders; and analyzes and evaluates national needs and research opportunities and provides advice to the Institute Director on matters of scientific interest. Core Facilities: * Functional MRI Core * Magnetic Resonance Core * Magnetoencephalography Core * Microarray Core * Neurophysiology Imaging Facility * Non-Human Primate Core * Scientific and Statistical Computing Core * Section on Instrumentation Core * Transgenic Core * Veterinary Medicine Resources |
has parent organization: National Institute of Mental Health is parent organization of: Genes Cognition and Psychosis Program is parent organization of: NIMH CORTEX is parent organization of: NIMH DIRP Scientific and Statistical Computing Core is parent organization of: NIMH Intramural Research Program Clinical Brain Disorders Branch |
NIMH | nlx_143686 | SCR_006860 | NIMH DIRP, Division of Intramural Research Programs at the National Institute of Mental Health, National Institute of Mental Health Intramural Research Program, DIRP at the NIMH, NIMH Intramural Research Program | 2026-07-27 09:32:40 | 3 | ||||||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | web service, web application, data access protocol, software resource | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-07-27 09:32:39 | 2760 | ||||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | software application, workflow software, software resource, data processing software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-07-27 09:31:08 | 11 | |||
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Mouse Brain Library Resource Report Resource Website 10+ mentions |
Mouse Brain Library (RRID:SCR_001112) | MBL | atlas, video resource, database, topical portal, image collection, portal, data or information resource | Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies. | brain, gene, genome, strain, c57bl/6j, dba/2j, a/j, genetic variant, phenotype, hippocampus, cerebellum, striatum, olfactory bulb, thalamus, neocortex, dorsal nucleus of lateral geniculate body, central nervous system |
is related to: Videoscribbler has parent organization: University of Tennessee Health Science Center; Tennessee; USA is parent organization of: MBL Pivot Collection is parent organization of: Mouse Brain Atlases |
NIMH P20 MH62009 | PMID:10857184 PMID:15043219 |
Restricted | nif-0000-00030 | SCR_001112 | MBL - Mouse Brain Library, Mouse Brain Library, The Mouse Brain Library | 2026-07-27 09:31:07 | 24 | |||||
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Clarity resources Resource Report Resource Website 10+ mentions |
Clarity resources (RRID:SCR_001387) | CLARITY Resources | video resource, training resource, experimental protocol, narrative resource, data or information resource | Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. | workshop, protocol, specimen preparation, transparent brain, glass brain, brain, neuroimaging, phenotyping, tissue, brain tissue, cortex, hippocampus, thalamus, ventral, brainstem |
is used by: NIF Data Federation is used by: Integrated Videos has parent organization: Stanford University; Stanford; California |
NIMH 4R01MH099647-05 | PMID:23575631 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152559 | SCR_001387 | Clarity resource | 2026-07-27 09:31:11 | 18 | |||||
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OBART Resource Report Resource Website 1+ mentions |
OBART (RRID:SCR_001903) | OBART | atlas, web application, data or information resource, software resource | Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases. | atlas, brain, clinical, mapping, meta-analysis, neuroscience, visualization, label |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Architecture Project has parent organization: Boston University; Massachusetts; USA |
NIMH 5R01MH084802 | PMID:19787067 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10473 | http://www.nitrc.org/projects/obart | http://obart.brainarchitecture.org | SCR_001903 | The Online Brain Atlas Reconciliation Tool, Online Brain Atlas Reconciliation Tool | 2026-07-27 09:31:23 | 2 | |||
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NIMH Data Archive Resource Report Resource Website 100+ mentions |
NIMH Data Archive (RRID:SCR_004434) | NDA | service resource, database, storage service resource, data repository, data or information resource | The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI). | afni brik, ascii, bshort, bfloat, connectome file format, cifti, clinical neuroinformatics, cor, dicom, imaging genomics, inc, minc2, nifti, os independent, philips par/rec, tex, vrml, phenotype, neuroimaging, genomic, gender, male, female, dti, fmri, mri, spectroscopy, eeg, microarray, snp, cnv, next-generation sequencing, gene regulation, gene expression, genotyping, pedigree, clinical assessment, FASEB list |
uses: HED Tags is used by: National Database for Clinical Trials related to Mental Illness is used by: RDoCdb is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: National Database for Clinical Trials related to Mental Illness is related to: RDoCdb has parent organization: National Institute of Mental Health hosts: GUID Tool |
Autism, Autism spectrum disorder, Asperger Syndrome, Normal control, Sibling control, Parental control, Fragile X syndrome | NIMH ; NINDS ; NIEHS ; NICHD ; Center for Information Technology |
Restricted | nlx_143735, r3d100010717, r3d100012653 | http://www.nitrc.org/projects/ndarportal, https://data-archive.nimh.nih.gov/, https://doi.org/10.17616/R37K63, https://doi.org/10.17616/R3XV5P | http://ndar.nih.gov/ | SCR_004434 | NDAR, National Database for Autism Research, National Institute of Mental Health Data Archive, National Database for Autism Research (NDAR) | 2026-07-27 09:32:01 | 291 | |||
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TrackVis Resource Report Resource Website 100+ mentions |
TrackVis (RRID:SCR_004817) | TrackVis | data visualization software, image analysis software, software resource, software application, image reconstruction software, image processing software, data processing software, software toolkit | TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux. | mri, dti, diffusion spectrum image, diffusion imaging, image reconstruction, diffusion mr fiber tracking, visualization, analyze, c++, console (text based), dicom, fiber tracking, image reconstruction, linux, macos, microsoft, magnetic resonance, nifti, posix/unix-like, tractography, visualization, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CAMINO-TRACKVIS |
MGH GCRC ; NIMH 5R01MH064044 |
Free for academic and non-profit research use, Non-commercial, For other purposes, Please contact them | nlx_143916 | SCR_004817 | TrackVis and Diffusion Toolkit | 2026-07-27 09:32:08 | 491 |
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