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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Rhesus Macaque Brain Atlases Resource Report Resource Website |
Rhesus Macaque Brain Atlases (RRID:SCR_017533) | data set, data or information resource, atlas | Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque. | Collection, atlas, data, scan, functional, structural, imaging, rhesus macaque | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | http://brainmap.wisc.edu/monkey.html | SCR_017533 | 2026-02-16 09:49:15 | 0 | |||||||||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | software development tool, software application, software development environment, community building portal, software resource, portal, data or information resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-02-16 09:48:33 | 24 | ||||
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AngioCalc Cerebral Aneurysm Calculator Resource Report Resource Website 1+ mentions |
AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) | AngioCalc | software application, software resource, data management software | Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images. | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155693 | SCR_012805 | AngioCalc Cerebral and Peripheral Aneurysm Calculator, AngioCalc Cerebral Aneurysm Calculator | 2026-02-16 09:48:30 | 9 | |||||||||
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USC Multimodal Connectivity Database Resource Report Resource Website 10+ mentions |
USC Multimodal Connectivity Database (RRID:SCR_012809) | UMCD | data repository, database, storage service resource, service resource, data or information resource | Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. | fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: MGH-USC Human Connectome Project |
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease | NRSA ; NIH Blueprint for Neuroscience Research ; NIA F31AG035438-01; NIDA HHSN271200800035C |
PMID:23226127 PMID:20850551 |
The community can contribute to this resource, Some features require an account | nlx_83091 | http://www.nitrc.org/projects/umcd | http://jessebrown.webfactional.com/welcome/default/index | SCR_012809 | UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database | 2026-02-16 09:48:17 | 25 | ||
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LiverSegm Resource Report Resource Website |
LiverSegm (RRID:SCR_013108) | LiverSegm | software application, data processing software, image processing software, image analysis software, software resource, segmentation software | A set of tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation. | liver segmentation, image processing software, injury segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP |
Free | nlx_155788 | SCR_013108 | 2026-02-16 09:48:20 | 0 | ||||||||
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Mixed Effect Model of Genetic-Set and Environment Interaction Resource Report Resource Website |
Mixed Effect Model of Genetic-Set and Environment Interaction (RRID:SCR_015514) | software resource, model, data or information resource, software toolkit | MATLAB Toolbox which provides a mixed effect model for gene-environment interaction (MixGE) on neuroimaging phenotypes, such as structural volumes and tensor-based morphometry (TBM). This model incorporates both fixed and random effects of genetic-set and environment interaction in order to investigate homogeneous and heterogeneous contributions of sets of genetic variants and their interactions with environmental risks to phenotypes. | gene environment interaction, gene environment interaction model, neuroimaging phenotype |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National University of Singapore; Singapore; Singapore |
Singapore National Research Foundation Singapore-NMRC/TCR/004-NUS/2008; Singapore National Research Foundation Singapore-NMRC/TCR/012-NUHS/2014; Singapore Ministry of Health National Medical Research Council NMRC/CBRG/0039/2013; Singapore Ministry of Education Academic Research Fund Tier 2 MOE2012-T2-2-130 |
Free for non-commercial use | SCR_015514 | Mixed Effect Model of Genetic Set and Environment Interaction, Mixed Effect Model of Genetic Set and Environment Interaction Toolbox, MixGE Toolbox | 2026-02-16 09:48:49 | 0 | ||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | software application, data processing software, software toolkit, data analysis software, software resource | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-02-16 09:49:00 | 1 | ||||||
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User Friendly Functional Connectivity - UF²C Resource Report Resource Website 1+ mentions |
User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) | UF²C | software application, data processing software, software toolkit, data analysis software, image analysis software, software resource | Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters. | standardize, functional, connectivity, brain, magnetic, resonance, imaging, graphical, user, interface, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MATLAB |
FAPESP | Free, Available for download, Freely available | SCR_016550 | User Friendly Functional Connectivity | 2026-02-16 09:49:03 | 1 | |||||||
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BrainNet Viewer Resource Report Resource Website 500+ mentions |
BrainNet Viewer (RRID:SCR_009446) | BrainNet Viewer | software application, data processing software, data visualization software, software resource | 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 | 2026-02-16 09:47:24 | 605 | ||||||||
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Cytoseg Resource Report Resource Website 1+ mentions |
Cytoseg (RRID:SCR_009553) | Cytoseg | software application, data processing software, image analysis software, software resource, segmentation 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 | 2026-02-16 09:47:26 | 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, data processing software, image analysis software, software resource, segmentation 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 | 2026-02-16 09:48:31 | 1 | ||||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | software application, data processing software, software toolkit, image processing software, image analysis software, software resource | 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. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science works with: VisuAlign |
Free, Available for download, Freely available | SCR_017183 | Neuroimaging utilities | 2026-02-16 09:49:11 | 25 | ||||||||
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MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | software application, data processing software, data visualization software, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/ http://www.mccauslandcenter.sc.edu/mricro/ http://www.nitrc.org/projects/mricron http://neuro.debian.net/pkgs/mricron.html https://bio.tools/MRIcron |
SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-02-16 09:45:46 | 2194 | |||||
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DPARSF Resource Report Resource Website 500+ mentions |
DPARSF (RRID:SCR_002372) | DPARSF | data processing software, software application, software toolkit, software resource | 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 | 2026-02-16 09:45:43 | 564 | |||||
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Statistical non-Parametric Mapping Resource Report Resource Website 50+ mentions |
Statistical non-Parametric Mapping (RRID:SCR_002092) | SnPM | data processing software, software application, software toolkit, software resource | 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 | 2026-02-16 09:45:41 | 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 | data processing software, software application, software resource, software toolkit | 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 | 2026-02-16 09:45:42 | 2 | |||||||
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Grantees Meeting for NITRC Resource Report Resource Website |
Grantees Meeting for NITRC (RRID:SCR_000419) | data or information resource, project portal, 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 | 2026-02-16 09:45:15 | 0 | ||||||||
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Mindboggle Resource Report Resource Website 100+ mentions |
Mindboggle (RRID:SCR_002438) | Mindboggle | data processing software, software application, software resource | 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 | 2026-02-16 09:45:47 | 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, project portal, 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 | 2026-02-16 09:45:39 | 20 | ||||
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I/OWA Resource Report Resource Website |
I/OWA (RRID:SCR_000858) | I/OWA | data processing software, software application, software resource, image analysis 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 | 2026-02-16 09:45:21 | 0 |
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