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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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, data processing software, segmentation software, image analysis software, software resource, registration 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 | 2026-08-03 09:32:43 | 472 | |||||
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BrainLiner Resource Report Resource Website 1+ mentions |
BrainLiner (RRID:SCR_004951) | BrainLiner | data repository, data or information resource, software toolkit, database, software application, storage service resource, software library, service resource, software resource | 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 | 2026-08-03 09:32:49 | 7 | |||||
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OpenNeuro Resource Report Resource Website 100+ mentions |
OpenNeuro (RRID:SCR_005031) | OpenNeuro, OpenfMRI | data repository, data or information resource, database, image repository, storage service resource, 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 | 2026-08-03 09:32:35 | 247 | ||||
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SINOMO Resource Report Resource Website |
SINOMO (RRID:SCR_005286) | SINOMO | software resource, data processing software, software application, data analysis software | Analysis-tool which identifies singular node motifs in a network. Network nodes can be described by node-motifs. It is an improvement to the method described in Costa et al. (2009). | network, network analysis, network motif, computational neuroscience, eeg, meg, electrocorticography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
EPSRC EP/G03950X/1; EPSRC EP/E002331/1; Korea Ministry of Education Science and Technology R32-10142; CNPq 301303/06-1; FAPESP 05/00587-5; FAPESP 2007/50633-9 |
PMID:21297963 | Creative Commons Attribution-NonCommercial License | nlx_144325 | http://www.nitrc.org/projects/sinomo | SCR_005286 | SINOMO (SIngular NOde MOtifs), Singular Node Motifs, SIngular NOde MOtifs | 2026-08-03 09:32:38 | 0 | ||||
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1000 Functional Connectomes Project Resource Report Resource Website 10+ mentions |
1000 Functional Connectomes Project (RRID:SCR_005361) | INDI, 1000 FCP, FCP | image collection, data repository, portal, data or information resource, database, image repository, catalog, storage service resource, service resource, project portal | Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets. | resting state functional mri, fmri, brain, neuroimaging, phenotype, function, data sharing, human, mri, r-fmri, rs-fmri, fc-fmri, rs--fcmri, resting-state, dicom, dti, child, adolescent, brain imaging, neuroinformatics, adult human, phenotype, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is used by: MetaSearch is listed by: NITRC-IR is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: NIH Data Sharing Repositories is affiliated with: Preprocessed Connectomes Project is related to: Spanish Resting State Network is related to: NITRC-IR is related to: NIH Data Sharing Repositories is related to: BASH4RfMRI is related to: 1000 Functional Connectomes Project has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: C-PAC is parent organization of: Neuro Bureau - Berlin Mind and Brain Sample is parent organization of: Quiron-Valencia Sample is parent organization of: ABIDE is parent organization of: Consortium for Reliability and Reproducibility is parent organization of: ADHD-200 Sample is parent organization of: FCP Classic Data Sharing Samples is parent organization of: NKI/Rockland Sample is parent organization of: NYU Institute for Pediatric Neuroscience Sample is parent organization of: Virginia Tech Carilion Research Institute Sample is parent organization of: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is parent organization of: Beijing: Eyes Open Eyes Closed Study is parent organization of: Beijing: Short TR Study is parent organization of: COBRE |
NITRIC | PMID:23133413 PMID:23123682 |
Restricted | SCR_015771, nlx_144428, r3d100011565, r3d100011555 | http://www.nitrc.org/projects/fcon_1000/, https://doi.org/10.17616/R3W05R, https://doi.org/10.17616/R35H0H | SCR_005361 | INDI, International Neuroimaging Data-Sharing Initiative, fcon_1000, Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI), 1000 Functional Connectomes Project, FCP/INDI | 2026-08-03 09:32:52 | 46 | ||||
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Internet Analysis Tools Registry Resource Report Resource Website 1+ mentions |
Internet Analysis Tools Registry (RRID:SCR_005638) | IATR | software application, data processing software, software resource, image analysis software, software repository | A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web. | database, tool, neuroimaging, image, analysis |
lists: Extensible MATLAB Medical image Analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
Human Brain Project | Public Domain | nlx_146252 | SCR_005638 | IATR - Internet Analysis Tools Registry | 2026-08-03 09:32:54 | 1 | ||||||
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ADHD-200 Sample Resource Report Resource Website 10+ mentions |
ADHD-200 Sample (RRID:SCR_005358) | ADHD-200, | portal, disease-related portal, topical portal, data or information resource, data set | A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU) | mri, fmri, brain, neuroimaging, attention deficit-hyperactivity disorder, anatomical, resting state functional mri, child, adolescent, human, young, early adult human, functional imaging, structural imaging, normal, normal control |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuro Bureau has parent organization: 1000 Functional Connectomes Project is parent organization of: ADHD-200 Preprocessed Data |
Attention deficit-hyperactivity disorder | Account required, Acknowledgement requested, Non-commercial | nlx_144426 | SCR_005358 | ADHD-200 Consortium | 2026-08-03 09:32:40 | 20 | ||||||
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CBRAIN Resource Report Resource Website 10+ mentions |
CBRAIN (RRID:SCR_005513) | CBRAIN | production service resource, data analysis service, storage service resource, analysis service resource, service resource, software resource | A flexible software platform for distributed processing, analysis, exchange and visualization of brain imaging data. The expected result is a middleware platform that will render the processing environment (hardware, operating systems, storage servers, etc...) transparent to a remote user. Interaction with a standard web browser allows application of complex algorithm pipelines to large datasets stored at remote locations using a mixture of network available resources such as small clusters, neuroimaging tools and databases as well as Compute Canada's High Performance Computing Centers (HPC). Though the focus of CBRAIN is providing tools for use by brain imaging researchers, the platform is generalizable to other imaging domains, such as radiology, surgical planning and heart imaging, with profound consequences for Canadian medical research. CBRAIN expanded its concept to include international partners in the US, Germany and Korea. As of December 2010, GBRAIN has made significant progress with the original three partners and has developed new partners in Singapore, China, India, and Latin America. CBRAIN is currently deployed on 6 Compute Canada HPC clusters, one German HPC cluster and 3 clusters local to McGill University Campus, totaling more than 80,000 potential CPU cores. | brain, neuroimaging, imaging, middleware, platform, network, data sharing, web application, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada is parent organization of: Latin American Brain Mapping Network (LABMAN) |
Free | nlx_144612 | http://www.nitrc.org/projects/cbrain | SCR_005513 | 2026-08-03 09:32:53 | 30 | |||||||
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3D Slicer Resource Report Resource Website 1000+ mentions |
3D Slicer (RRID:SCR_005619) | Slicer | software application, data processing software, image analysis software, software resource, data visualization software | A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl. | birn, diffusion, functional, na-mic (ncbc), nifti-1 support, registration, segmentation, visualization, volume, warping |
uses: 3DSlicerLupusLesionModule uses: ShapePopulationViewer uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Slicer3 Example Modules is related to: Stereoscopic Atlas of Intrinsic Brain Networks is related to: VMTK in 3D Slicer is related to: Diffusion Tractography with Kalman Filter is related to: Fast Nonlocal Means for MRI denoising is related to: SpineSegmentation module for 3DSlicer is related to: BioImage Suite is related to: NA-MIC Kit is related to: Hammer And WML Modules for 3D Slicer is related to: ABC (Atlas Based Classification) is related to: ARCTIC is related to: Finsler tractography module for Slicer is related to: GAMBIT is related to: GPU based affine registration is related to: GTRACT is related to: LEAD-DBS has parent organization: Harvard University; Cambridge; United States is parent organization of: Level-set Segmentation for Slicer3 is parent organization of: Slicer3 Module Rician noise filter has plug in: MultiXplore works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: SlicerMorph |
NIH ; NCRR ; NIBIB ; NCI ; US Army ; Telemedicine and Advanced Technology Research Center |
3D Slicer License | nif-0000-00256 | http://www.nitrc.org/projects/slicer | SCR_005619 | Slicer, 3D Slicer: A multi-platform free and open source software package for visualization and medical image computing, 3D Slicer, 3DSlicer | 2026-08-03 09:32:54 | 2238 | |||||
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DPARSF Resource Report Resource Website 500+ mentions |
DPARSF (RRID:SCR_002372) | DPARSF | software toolkit, software resource, software application, data processing software | A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely. | magnetic resonance, fmri, resting-state fmri, matlab, analysis, brain |
is used by: DPABI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: RFMRI.ORG |
PMID:20577591 | GNU General Public License | nlx_155735 | http://www.nitrc.org/projects/dparsf | SCR_002372 | Data Processing Assistant for Resting-State fMRI | 2026-08-03 09:31:40 | 564 | |||||
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NiftyRec Resource Report Resource Website 1+ mentions |
NiftyRec (RRID:SCR_002499) | NiftyRec | software toolkit, software resource, software application, data processing software | Software toolbox that includes reconstruction tools for emission and transmission imaging modalities, including Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), cone-beam X-Ray CT and parallel-beam X-Ray CT. At the core of NiftyRec are efficient, GPU accelerated, projection, back-projection and iterative reconstruction algorithms. The easy to use Matlab and Python interfaces of NiftyRec enable fast prototyping and development of reconstruction algorithms. NiftyRec includes standard iterative reconstruction algorithms such as Maximum Likelihood Expectation Maximisation (MLEM), Ordered Subsets Expectation Maximisation (OSEM) and One Step Late Maximum A Posteriori Expectation Maximisation (OSL-MAPEM), for multiple imaging modalities. | computed tomography, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
BSD License | nlx_155898 | http://www.nitrc.org/projects/niftyrec | SCR_002499 | NiftyRec Tomography Toolbox, NiftyRec Open Source Tomography Toolbox | 2026-08-03 09:31:43 | 2 | ||||||
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Statistical non-Parametric Mapping Resource Report Resource Website 50+ mentions |
Statistical non-Parametric Mapping (RRID:SCR_002092) | SnPM | software toolkit, software resource, software application, data processing software | A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM. | analyze, linear, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, regression, statistical operation, sunos/solaris, windows, statistical parametric mapping, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: SPM has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Warwick; Coventry; United Kingdom |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00342 | http://www.nitrc.org/projects/snpm | SCR_002092 | SnPM: Statistical nonParametric Mapping, SnPM - Statistical NonParametric Mapping - A toolbox for SPM, Statistical nonParametric Mapping | 2026-08-03 09:31:33 | 95 | |||||
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Wavelet-based Image Fusion Resource Report Resource Website 1+ mentions |
Wavelet-based Image Fusion (RRID:SCR_002007) | Wavelet-based Image Fusion | software toolkit, software resource, software application, data processing software | Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012). | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:21761448 | Free, Available for download, Freely available | nlx_156018 | SCR_002007 | 2026-08-03 09:31:36 | 2 | |||||||
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Grantees Meeting for NITRC Resource Report Resource Website |
Grantees Meeting for NITRC (RRID:SCR_000419) | data or information resource, portal, project portal | This project is meant for planning the NITRC Grantee meetings. A website for organizing meetings for the Neuroimaging Informatics Tools and Resources Clearinghouse, to facilitate participants meeting one another, and promote discussion of common interests and collaboration. | meeting, neuroimaging, nitrc, informatics, tools, collaboration, discussion | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | nlx_155875, SCR_014081 | http://www.nitrc.org/plugins/mwiki/index.php/nihgrantees:2009Meeting | SCR_000419 | 2026-08-03 09:31:02 | 0 | ||||||||
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Mindboggle Resource Report Resource Website 100+ mentions |
Mindboggle (RRID:SCR_002438) | Mindboggle | software resource, software application, data processing software | Mindboggle (http://mindboggle.info) is open source software for analyzing the shapes of brain structures from human MRI data. The following publication in PLoS Computational Biology documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350 | analyze, anatomic, atlas application, console (text based), labeling, python, magnetic resonance, os independent, region of interest, segmentation, brain, label, mri, anatomy, cerebral cortex, human brain, parcellation, morphometry, shape measures, cortical thickness, cortical depth, Laplace-Beltrami spectra, Zernike moments | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIMH MH084029-02 | Free, Available for download, Freely available | nlx_155813 | http://www.nitrc.org/projects/mindboggle | SCR_002438 | 2026-08-03 09:31:57 | 211 | ||||||
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Neural ElectroMagnetic Ontologies (NEMO) Project Resource Report Resource Website 10+ mentions |
Neural ElectroMagnetic Ontologies (NEMO) Project (RRID:SCR_002001) | NEMO | data or information resource, portal, project portal | THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, classification, labeling, eeg, event-related potential, meg, rdf, metadata standard, decomposition, segmentation, extraction, brain, electromagnetic, electrocorticography, information specification, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Oregon; Oregon; USA is parent organization of: NEMO Ontology |
PMID:22180824 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10899 | http://www.nitrc.org/projects/nemo, https://sourceforge.net/projects/nemoontologies/ | http://nemo.nic.uoregon.edu | SCR_002001 | Neural ElectroMagnetic Ontologies | 2026-08-03 09:31:30 | 20 | ||||
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I/OWA Resource Report Resource Website |
I/OWA (RRID:SCR_000858) | I/OWA | image analysis software, software resource, software application, data processing software | Software for real-time parametric statistical analysis of functional MRI (fMRI) data. The system that combines a general architecture for sampling and time-stamping relevant information channels in fMRI (image acquisition, stimulation, subject responses, cardiac and respiratory monitors, etc.) and an efficient approach to manipulating these data, featuring incremental subsecond multiple linear regression. The advantages of the system are the simplification of event timing and efficient and unified data formatting. Substantial parametric analysis can be performed and displayed in real-time. Immediate (replay) and delayed off-line analysis can also be performed with the same interface. The system provides a time-accounting infrastructure that readily supports standard and innovative approaches to fMRI. | fmri, real-time, multiple linear regression, brain mapping |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Iowa; Iowa; USA |
PMID:11180437 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155643 | SCR_000858 | Input/Output time-aWare Architecture, Input / Output time aWare Architecture, I/OWA 3 | 2026-08-03 09:31:11 | 0 | ||||||
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NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification Resource Report Resource Website 500+ mentions |
NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification (RRID:SCR_002074) | image analysis software, software resource, software application, data processing software | NeuronJ is an ImageJ plugin to facilitate the tracing and quantification of elongated structures in two-dimensional (2D) images (8-bit gray-scale and indexed color), in particular neurites in fluorescence microscopy images. Sponsors: The development of NeuronJ started while the primary developer ( Dr. Erik Meijering, PhD) was with the Biomedical Imaging Group (collaborating with people from the Laboratory of Cellular Neurobiology) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, and was finished while Dr. Meijering was with the Biomedical Imaging Group Rotterdam in the Netherlands. | fluorescence, application, imaging processing software, java, measurement, microscope, microscopy, neurite, neuroinformatics, neuron, plugin, statistic, two-dimentional, image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
Free, Available for download, Freely available | nif-0000-00108 | http://www.nitrc.org/projects/neuronj | SCR_002074 | NeuronJ | 2026-08-03 09:31:32 | 966 | |||||||
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NIF Data Federation Resource Report Resource Website 10+ mentions |
NIF Data Federation (RRID:SCR_004834) | Data Federation | service resource, data or information resource, portal | Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below. | semantics, neuroscience, animal, annotation, antibody, biospecimen, brain activation foci, clinical trial, connectivity, dataset, disease, drug, grant, image, microarray, model, multimedia, negative data, pathway, people, plasmid, registry, software, brain region, cell, gene, molecule, multi-level, nervous system, nervous system function, model |
uses: MNI Podcasts uses: Educational Resources in Neuroscience uses: Mind Hacks uses: BAMS Nested Regions uses: Indeed uses: NINDS Disorder Index uses: Drug Design Data Resource uses: PubMed Health uses: This Week In Science uses: Science Talk uses: BAMS Connectivity uses: Lady Scientist uses: Psychology Corner uses: Wired Science uses: CENtral Science uses: RetractionWatch.com uses: The Guardian: Science Weekly uses: H2SO4Hurts uses: 60-Second Mind uses: PLoS Blogs uses: Clarity resources uses: Open Source Brain uses: Diabetic Complications Consortium uses: Integrated Animals uses: Kawasaki Disease Dataset uses: EEGbase uses: Integrated Models uses: Lifespan Observations Database uses: NIF Web Services uses: NIF Blog uses: ATCC uses: Cerebellar Platform uses: Brain Machine Interface Platform uses: Rafael Yustes Laboratory uses: ASAP uses: NIH VideoCasting uses: NIDA Data Share uses: Neurofed uses: Candida Genome Database uses: Addgene uses: ASPGD uses: Glomerular Activity Response Archive uses: WikiPathways uses: AmiGO uses: NeuroMorpho.Org uses: Cell Centered Database uses: Integrated uses: Community Structure-Activity Resource uses: ClinicalTrials.gov uses: Ensembl uses: GeneNetwork uses: Avian Brain Circuitry Database uses: EcoCyc uses: Entrez Gene uses: Zebrafish Information Network (ZFIN) uses: Arredondo ANT fNIRS dataset1 uses: Grants.gov uses: T3DB uses: Simtk.org uses: PharmGKB uses: DrugBank uses: Aging Genes and Interventions Database uses: Gene Expression Nervous System Atlas uses: SumsDB uses: bioDBcore uses: BioNumbers uses: Gene Ontology uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Gramene uses: Retina Project uses: HomoloGene uses: ArrayExpress uses: Journal of Visualized Experiments uses: Allen Mouse Brain Reference Atlas uses: Gene Weaver uses: Visiome Platform uses: Developmental Therapeutics Program uses: NeuroMab uses: WormBase uses: NeuronDB uses: Integrated Grants uses: studyforrest.org uses: BrainInfo uses: Mouse Phenome Database (MPD) uses: NCBI Taxonomy uses: NCBI Protein Database uses: Psychoactive Drug Screening Program Ki Database uses: Nuclear Receptor Signaling Atlas uses: Brede Database uses: NeuroImaging Tools and Resources Collaboratory (NITRC) uses: Mouse Genome Informatics Transgenes uses: Reactome uses: Cell Image Library (CIL) uses: BAMS Cells uses: Synapse Web uses: Integrated Videos uses: NeuroVault uses: Royal College of Psychiatrists Podcasts uses: WU-Minn HCP 500 Subjects MR and MEG Release uses: Data.gov Science and Research Data Catalog uses: NITRC-IR uses: One Mind Biospecimen Bank Listing uses: Integrated Brain Gene Expression uses: BrainSpan uses: All In The Mind uses: Scientific American Cross-Check uses: PubChem uses: NeuroPod uses: BrainSpan uses: Health.Data.gov uses: Biointeractive uses: UniProtKB uses: Gray Matters uses: dkCOIN uses: Brain Science Podcast uses: NIGMS Human Genetic Cell Repository uses: DISCO uses: GeneDB Lmajor uses: TAIR uses: ScienceNOW uses: Daily Scan uses: SGD uses: Integrated Software uses: BrainPod uses: GeneDB Tbrucei uses: MPO uses: PANTHER uses: Neurology Podcast uses: Integrated Disease uses: VMD uses: UCSF Laboratory for Visual Neuroscience uses: NIMH Chemical Synthesis and Drug Supply Program uses: NIH Neuroscience Microarray Consortium uses: SGN uses: Protocol Online - Your labs reference book uses: Integrated Podcasts uses: OpenNeuro uses: National Academy of Sciences Podcasts uses: Beta Cell Biology Consortium uses: Naturejobs uses: Scientific American Guest Blog uses: jobs.ac.uk uses: New Scientist Jobs uses: Science Careers uses: Access-ScienceJobs.co.uk uses: ScienceBlogs: Life Science uses: ScienceBlogs: Brain and Behavior uses: TheScienceJobs.com uses: Nature Network Blogs uses: The Guardian: Science uses: LabSpaces uses: ScienceBlogs: Medicine and Health uses: Scientific American Observations uses: Scientific American Bering in Mind uses: QUEST uses: Daring Nucleic Adventures - genegeek uses: Oxford Science Blog uses: Sciblogs uses: New York Times - Well uses: SciLogs uses: Cassandras Tears uses: BioPortfolio uses: Now at NEJM uses: 1000 Functional Connectomes Project uses: Integrated Jobs uses: Integrated Blogs uses: JCVI CMR uses: SciCrunch Registry uses: Neuroskeptic uses: CRCNS uses: Expression Atlas of the Marmoset uses: IXI dataset uses: Integrated Auto-Extracted Annotation uses: EU Clinical Trials Register uses: Integrated Clinical Trials uses: Human Brain Atlas uses: goCognitive uses: Law and Neuroscience uses: International Mouse Phenotyping Consortium (IMPC) uses: ClinVar uses: Integrated Gene-Disease Interaction uses: XNAT Central uses: neuroelectro uses: Integrated Nervous System Connectivity uses: Antibody Registry uses: OMIA - Online Mendelian Inheritance in Animals uses: OMIM uses: Science Podcast uses: Mouse Genome Informatics (MGI) uses: Monster uses: NCBI uses: Wired Science Blogs uses: F1000 Posters uses: Neurophilosophy uses: Comparative Toxicogenomics Database (CTD) uses: FlyBase uses: GeneReviews uses: GeneDB Pfalciparum uses: Naturally Selected uses: PomBase uses: Pseudomonas Genome Database uses: The Guardian: Science Videos uses: Orphanet uses: Dictyostelium discoideum genome database uses: PeptideAtlas uses: NeuroSynth uses: neuropathology blog uses: Genomes Unzipped uses: National Institutes of Health Research Portfolio Online Reporting Tool uses: BrainMaps.org uses: It Takes 30 uses: Gait in Parkinson's Disease uses: Physiobank uses: Gait Dynamics in Neuro-Degenerative Disease Data Base uses: American Journal of Psychiatry Podcasts uses: Neurodatabase.org uses: Brain Architecture Management System uses: RanchoBiosciences uses: ModelDB uses: CoCoMac uses: Olfactory Bulb Odor Map DataBase (OdorMapDB) uses: Gene Expression Omnibus uses: Caenorhabditis Genetics Center uses: Labome uses: Open Access Series of Imaging Studies uses: Biological General Repository for Interaction Datasets (BioGRID) uses: Olfactory Receptor DataBase uses: T1DBase uses: Gemma uses: CellML Model Repository uses: ResearchCrossroads uses: Biocompare uses: BioNOT uses: Hays uses: Research Blogging uses: Discover Magazine uses: PolygenicBlog uses: Kawasaki Disease Dataset2 uses: Allen Mouse Brain Connectivity Atlas uses: Integrated Manually Extracted Annotation uses: Roadmap Epigenomics Project uses: Integrated Cell Lines uses: National Mouse Metabolic Phenotyping Centers uses: Mendelspod uses: Integrated Snippets uses: Integrated Datasets uses: Nature Podcast uses: GWAS: Catalog of Published Genome-Wide Association Studies uses: KEGG uses: USC Multimodal Connectivity Database uses: Inside NIA: A Blog for Researchers uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: NIF Registry Automated Crawl Data uses: Genetic Analysis Software uses: anage uses: Intestinal Stem Cell Consortium uses: Animal QTLdb uses: elements of morphology uses: Human Life-Table Database uses: Clinical Genomic Database uses: NIDDK Central Repository uses: MONARCH Initiative uses: Human Phenotype Ontology is used by: SciCrunch is used by: NIDDK Information Network (dkNET) lists: AutDB lists: Drug Related Gene Database lists: Gene Ontology Tools lists: CHEBI is listed by: 3DVC is related to: International Mouse Strain Resource is related to: Internet Brain Volume Database is related to: Resource Identification Portal is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: NIH Human Pluripotent Stem Cell Registry is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: Journal of Comparative Neurology Antibody database has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Refer to individual databases | nlx_81822 | http://neuinfo.org/nif/nifgwt.html?query=* | SCR_004834 | Neuroscience Information Framework Data Federation | 2026-08-03 09:32:44 | 28 | |||||
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Fusion ICA Toolbox Resource Report Resource Website 10+ mentions |
Fusion ICA Toolbox (RRID:SCR_003494) | FIT | software toolkit, software resource, software application, data processing software | A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 | analysis, functional magnetic resonance imaging, cca, image, eeg, neuroimaging, matlab, smri, snp, mri, algorithm, reusable library, independent component analysis, principal component analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of New Mexico; New Mexico; USA |
NIBIB 1RO1EB005846; NSF 0612076 |
GNU General Public License | nif-0000-36743 | http://www.nitrc.org/projects/fit | SCR_003494 | Fusion ICA Toolbox (FIT) | 2026-08-03 09:32:16 | 13 |
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