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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MCIC Resource Report Resource Website 10+ mentions |
MCIC (RRID:SCR_002310) | MCIC | data or information resource, data set | Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and gender and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). This data repository will be useful to 1) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data. | clinical neuroinformatics, dicom, magnetic resonance, image collection, clinical assessment, diagnose, healthy control, neuropsychological test, psychiatric disorder, schizoaffective disorder, schizophrenia, diffusion-weighted |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Mind Research Network - COINS |
Schizophrenia, Normal control | PMID:23760817 | COINS Data Use Agreement | nlx_155657 | SCR_002310 | 2026-07-27 09:31:30 | 33 | ||||||
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ABIDE Resource Report Resource Website 100+ mentions |
ABIDE (RRID:SCR_003612) | ABIDE | data or information resource, data set | Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included. | phenotype, resting state functional magnetic resonance imaging, mri, image, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Autism spectrum disorder, Normal | Leon Levy Foundation ; Joseph P. Healy ; Stavros Niarchos Foundation ; NIMH K23MH087770; NIMH R03MH096321 |
Account required, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | nlx_157761 | SCR_003612 | Autism Brain Imaging Data Exchange | 2026-07-27 09:31:49 | 212 | |||||
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Registry Builder Data Harmonization and Aggregation Tool Resource Report Resource Website |
Registry Builder Data Harmonization and Aggregation Tool (RRID:SCR_006559) | Registry Builder Data Harmonization and Aggregation Tool | commercial organization, software resource | Software to harmonize the data that you have in different Excel files, databases, repositories, biospecimen applications, etc. and maps it to one common registry. Remedy Informatics' platform aggregates data from multiple sources, harmonizes the data via Ontology, and provides data visualization and pattern recognition and querying tools. | registry, ontology, visualization, pattern recognition, querying tool | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Mosaic License, Http://www.nitrc.org/include/glossary.php#694 | nlx_155942 | http://www.nitrc.org/projects/registrybuilder | SCR_006559 | 2026-07-27 09:32:35 | 0 | |||||||
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Brain Segmentation Testing Protocol Resource Report Resource Website |
Brain Segmentation Testing Protocol (RRID:SCR_009445) | Brain Segmentation Testing Protocol | data or information resource, data set | A free collection of MRI brain images for testing segmentation algorithms. It is available for download to assess the accuracy, reproducibility and sensitivity of MRI segmentation software. It includes data from infants and adults as well as patients with Alzheimer's disease. | analyze, magnetic resonance, nifti, oasis, segmentation, software, test data, image collection, mri, segmentation software, infant, adult human, child, alzheimer's disease, brain imaging, data set, research, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: King's College London; London; United Kingdom |
PMID:21835253 | Available for download | nlx_155588 | SCR_009445 | 2026-07-27 09:33:19 | 0 | |||||||
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BRAINSTestData Resource Report Resource Website |
BRAINSTestData (RRID:SCR_009517) | BRAINSTestData | data or information resource, data set | About 1.2GB of anonymized imaging data of many different file formats used by the BRAINS suite of tools (BRAINSFit, GTRACT, BRAINS, BRAINSTracer... and others) as a common set of anonymized data for nightly regression testing. | magnetic resonance, image collection, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
nlx_155704 | http://www.nitrc.org/projects/brainstestdata | SCR_009517 | 2026-07-27 09:33:20 | 0 | ||||||||
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EEG human categorization data Resource Report Resource Website |
EEG human categorization data (RRID:SCR_009468) | EEG human categorization data | data or information resource, data set | A collection of 32-channel data from 14 subjects (7 males, 7 females) acquired using the Neuroscan software. Subjects are performing a go-nogo categorization task and a go-no recognition task on natural photographs presented very briefly (20 ms). Each subject responded to a total of 2500 trials. Data is CZ referenced and is sampled at 1000 Hz (total data size is 4Gb; more details are given later). | eeg, meg, electrocorticography, male. female | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155616 | SCR_009468 | 2026-07-27 09:33:20 | 0 | ||||||||
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Diffusion MRI - In-vivo and Phantom Data Resource Report Resource Website 1+ mentions |
Diffusion MRI - In-vivo and Phantom Data (RRID:SCR_009464) | Diffusion MRI - In-vivo and Phantom Data | data or information resource, data set | An open-data initiative for the distributation of common datasets for the evaluation and validation of diffusion MRI processing methods. http://www.dkfz.de/en/medphysrad/projectgroups/dwi/DTI_projects.html#inhalt3 | magnetic resonance, nifti, nrrd |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: German Cancer Research Center works with: FIONA-QC-PHANTOM |
BSD/MIT-Style Open unspecified license License | nlx_155611 | SCR_009464 | 2026-07-27 09:33:19 | 2 | ||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | analysis service resource, service resource, data set, data or information resource, data repository, image repository, data analysis service, data access protocol, software resource, source code, production service resource, web service, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01 |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me, http://www.nitrc.org/projects/ocp/ | SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-07-28 09:40:56 | 7 | ||||
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neurodebian Resource Report Resource Website 10+ mentions |
neurodebian (RRID:SCR_004401) | NeuroDebian | software application, data distribution software, source code, software resource, data processing software, software development environment, software development tool, software repository | Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note. | linux, linux distribution, virtual machine, fmri, eeg, pymvpa, python, r, debian, brain image, neuroscience, platform, afni brik, bshort, bfloat, console (text based), dicom, domain independent, freebsd, gnome, kde, linux, minc2, nifti, philips par/rec, development environment, posix/unix-like, system administrator, web environment |
lists: MRIcron is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: NITRC Computational Environment is related to: PyMVPA is related to: MRtrix has parent organization: Debian has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany is parent organization of: VoxBo is parent organization of: Computational Morphometry Toolkit |
PMID:23055966 | GNU General Public License v3, The community can contribute to this resource | nlx_143723 | http://www.nitrc.org/projects/neurodebian | SCR_004401 | Debian Neuroscience Repository, neuro debian | 2026-07-28 09:41:01 | 40 | |||||
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ANTS - Advanced Normalization ToolS Resource Report Resource Website 100+ mentions |
ANTS - Advanced Normalization ToolS (RRID:SCR_004757) | ANTS, ANTsX | software application, software resource, data processing software, registration software, segmentation software, image analysis software | Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion. | algorithm, atlas application, morphology, segmentation, image registration, temporal transformation, child, pediatric, normalization |
is used by: CMIND PY is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Segmentation of Hippocampus Subfields is related to: ANTsR has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB006266 | PMID:20851191 PMID:33907199 |
nlx_75959 | http://www.nitrc.org/projects/ants, https://sources.debian.org/src/ants/, https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621 | SCR_004757 | Advanced Normalization Tools | 2026-07-28 09:41:06 | 472 | |||||
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BrainLiner Resource Report Resource Website 1+ mentions |
BrainLiner (RRID:SCR_004951) | BrainLiner | software application, service resource, data or information resource, data repository, database, software resource, software library, storage service resource, software toolkit | Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren''''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us | brain-machine interface, brain, behavior, neurophysiology, electromyography, fmri, speech, vision, memory, neuron, eeg, electrocorticography, food tracking task, food tracking, task, meg, mutielectrode, nirs, optical imaging, pet, time-series data, neuronal spike timing, data sharing, manipulation, data set, metadata standard, neuroscience, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroshare - Open data specifications and software for neurophysiology has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26858636 | GNU General Public License, The community can contribute to this resource | nlx_91840 | SCR_004951 | BrainLiner.jp | 2026-07-28 09:41:13 | 7 | |||||
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OpenNeuro Resource Report Resource Website 100+ mentions |
OpenNeuro (RRID:SCR_005031) | OpenNeuro, OpenfMRI | service resource, data or information resource, data repository, image repository, database, storage service resource | Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. | neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list |
uses: Brain Imaging Data Structure (BIDs) uses: HED Tags is used by: studyforrest.org is used by: DataLad is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is used by: Baby Open Brains is recommended by: National Library of Medicine is recommended by: BRAIN Initiative 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 listed by: DataCite is listed by: FAIRsharing is affiliated with: NEMAR is related to: Integrated Manually Extracted Annotation has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Reproducible Neuroscience has parent organization: BRAIN Initiative is provided by: OpenNeuro |
NSF OCI1131441; NIDA ; Laura and John Arnold Foundation ; Stanford ; Squishymedia ; BRAIN Initiative ; NIMH |
Free, Freely available | DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 | http://www.nitrc.org/projects/openfmri, https://github.com/OpenNeuroDatasets, https://doi.org/10.17616/R33047, https://doi.org/10.17616/r33047, https://doi.org/10.18112/, https://dx.doi.org/10.18112/, https://fairsharing.org/10.25504/FAIRsharing.s1r9bw, https://doi.org/10.17616/R33047 | http://openfmri.org | SCR_005031 | OpenfMRI, Open fMRI, OpenNeuro | 2026-07-28 09:41:12 | 247 | ||||
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SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | software application, data analysis software, software resource, data processing software, image analysis software | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12, https://bio.tools/SPM | https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-07-28 09:41:40 | 8694 | |||||
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ConnectomeDB Resource Report Resource Website 50+ mentions |
ConnectomeDB (RRID:SCR_004830) | ConnectomeDB | service resource, data or information resource, data repository, image repository, database, image collection, storage service resource | Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source. | brain, connectivity, human, adult human, evaluation, clinical, behavior, data set, diffusion imaging, resting-state fmri, task-evoked fmri, t1-weighted mri, t2-weighted mri, structural mapping, myelin mapping, magnetoencephalography, electroencephalography, fmri, twin |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: Washington University in St. Louis; Missouri; USA works with: Connectome Workbench |
Healthy, Twin, Non-twin sibling | NIH Blueprint for Neuroscience Research ; Washington University in St. Louis; Missouri; USA ; McDonnell Center for Systems Neuroscience ; NIMH 1U54MH091657 |
PMID:22366334 | Account required, Open unspecified license, Acknowledgement required, See Data Use Terms, The community can contribute to this resource | nlx_143923 | SCR_004830 | 2026-07-28 09:41:07 | 56 | |||||
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Biomedical Informatics Research Network Resource Report Resource Website 10+ mentions |
Biomedical Informatics Research Network (RRID:SCR_005163) | BIRN | service resource, data or information resource, data repository, database, software resource, atlas, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups. | dti, fmri, alzheimer's disease, cognitive impairment, collaborative environment, cyberinfrastructure, data sharing, depressive disorder, information technology, infrastructure, memory dysfunction, microarray, mri, neurodegenerative disease, neuroinformatics, neuroimaging, genetics, biomedical material, neurobiology, electrophysiology, collaboration, biomedical, imaging, imaging system, biomedical engineering, brain, health |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org is listed by: DataCite has parent organization: University of Southern California; Los Angeles; USA is parent organization of: Morphometry BIRN is parent organization of: Knowledge Engineering from Experimental Design is parent organization of: Mouse Biomedical Informatics Research Network is parent organization of: NIH Topic Maps - A Topic Database of NIH Funded Grants is parent organization of: Human Imaging Database is parent organization of: Function BIRN is parent organization of: B0 and eddy current correction for DTI is parent organization of: BrainSuite is parent organization of: Open Access Series of Imaging Studies |
NIH Blueprint for Neuroscience Research ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01; NIGMS U24 GM104203 |
PMID:21515543 PMID:18348946 PMID:17238407 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00027, r3d100010770 | http://www.nitrc.org/projects/birn, https://doi.org/10.17616/R3F02K | http://www.birncommunity.org/, https://neuroscienceblueprint.nih.gov/factSheet/birn.htm | SCR_005163 | BIRN - The Conduit for Biomedical Research, Biomedical Informatics Research Network - The Conduit for Biomedical Research | 2026-07-28 09:41:17 | 12 | |||
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SurfStat Resource Report Resource Website 100+ mentions |
SurfStat (RRID:SCR_007081) | SurfStat | software application, software toolkit, software resource, data processing software, image analysis software | A Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory. | afni brik, analyze, linear, matlab, minc, modeling, magnetic resonance, nifti, os independent, regression, statistical operation, pet, random field theory |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Free | nlx_156000 | http://www.nitrc.org/projects/surfstat | SCR_007081 | 2026-07-28 09:41:43 | 250 | |||||||
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BrainNet Viewer Resource Report Resource Website 500+ mentions |
BrainNet Viewer (RRID:SCR_009446) | BrainNet Viewer | data visualization software, software resource, software application, data processing software | Aa brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way. | linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, visualization, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155589 | SCR_009446 | 2026-07-28 09:42:18 | 605 | ||||||||
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Cytoseg Resource Report Resource Website 1+ mentions |
Cytoseg (RRID:SCR_009553) | Cytoseg | software application, software resource, data processing software, segmentation software, image analysis software | A tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. It works best for 3D blob shaped objects like mitochondria, lysosomes, etc. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools). | computational neuroscience, neuropil, 3d electron microscopy, electron microscopy | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155733 | http://www.nitrc.org/projects/cytoseg | SCR_009553 | 2026-07-28 09:42:27 | 1 | |||||||
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NIH-CIDI Lung Segmentation Tool Resource Report Resource Website 1+ mentions |
NIH-CIDI Lung Segmentation Tool (RRID:SCR_014150) | software application, software resource, data processing software, segmentation software, image analysis software | A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung. | segmentation software, lung, ct image, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
PMID:25570151 | Open source | SCR_014150 | CIDI-lung-seg, CIDI Lung Seg | 2026-07-28 09:43:44 | 1 | ||||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | software application, software toolkit, software resource, data processing software, image processing software, image analysis software | Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: VisuAlign |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:32973479 | Free, Available for download, Freely available | https://nutil.readthedocs.io; https://github.com/Neural-Systems-at-UIO/nutil | SCR_017183 | Neuroimaging utilities | 2026-07-28 09:44:27 | 25 |
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