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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Optseq Resource Report Resource Website 100+ mentions |
Optseq (RRID:SCR_014363) | data acquisition software, data processing software, software application, software resource, standalone software | Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be. | fmri, scheduling event, event, rper, hemodynamic response, stimulus, stochastic design | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_005976, nlx_151349 | http://www.nitrc.org/projects/optseq | SCR_014363 | Optseq2, Optseq - fMRI Event Scheduler | 2026-09-19 12:52:56 | 341 | |||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 50+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-09-19 12:53:00 | 50 | |||||||
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Group Sparse Canonical Correlation Analysis Resource Report Resource Website |
Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) | GSCCA | data analysis software, data processing software, software application, software resource | Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data. | group analysis, correlation analysis | has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) | NSF ; NIH |
Available for download | SCR_014977 | 2026-09-19 12:53:04 | 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) | data or information resource, model, software 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 | 2026-09-19 12:53:09 | 0 | ||||||||
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Faceted Search Based Ontology Visualizer Resource Report Resource Website |
Faceted Search Based Ontology Visualizer (RRID:SCR_000124) | ontologyviz | software resource | Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy. | computational neuroscience, magnetic resonance, ontology, functional neuroanatomy, facet, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | nlx_155874 | SCR_000124 | 2026-09-19 12:49:16 | 0 | ||||||||
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3DMeshMetric Resource Report Resource Website 1+ mentions |
3DMeshMetric (RRID:SCR_000043) | 3DMeshMetric | data processing software, data visualization software, software application, software resource | Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation. | visualize meshes, color, opacity, smoothing, down sampling, type of representation, | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155578 | SCR_000043 | 2026-09-19 12:49:14 | 2 | ||||||||
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Altered States Database Resource Report Resource Website 1+ mentions |
Altered States Database (RRID:SCR_016350) | ASDB | data or information resource, database | Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires. Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions. Is listed by Neuroimaging Informatics Tools. | altered, state, database, comprised, questionnaire, data, consciousness, neuroscience | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | VolkswagenStiftung ; Wikimedia Foundation ; Stifterverband |
DOI:10.17605/OSF.IO/8MBRU | Free, Freely available | http://alteredstatesdb.org/#focus | SCR_016350 | Altered States Database | 2026-09-19 12:57:35 | 2 | |||||
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dinifti Resource Report Resource Website 1+ mentions |
dinifti (RRID:SCR_000303) | dinifti | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format. | analyze, console (text based), dicom, format conversion, freebsd, linux, magnetic resonance, nifti, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: New York University; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155843 | http://www.nitrc.org/projects/dinifti, http://cbi.nyu.edu/software/dinifti.php, https://sources.debian.org/src/dicomnifti/ | SCR_000303 | NYU CBI DICOM to NIfTI Converter | 2026-09-19 12:57:41 | 2 | ||||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. | c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155961 | http://www.nitrc.org/projects/shapeworks | SCR_000424 | 2026-09-19 12:57:41 | 1 | ||||||
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CIFTI Connectivity File Format Resource Report Resource Website 1+ mentions |
CIFTI Connectivity File Format (RRID:SCR_000852) | CIFTI Connectivity File Format | software application, software resource, systems interoperability software | Standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties. Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats. Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155527 | SCR_000852 | Connectivity Informatics Technology Initiative Connectivity File Format | 2026-09-19 12:57:42 | 7 | |||||||
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Group Level Imputation of Statistic Maps Resource Report Resource Website |
Group Level Imputation of Statistic Maps (RRID:SCR_002397) | Group Level Imputation of Statistic Maps | software resource, software toolkit | A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R). | magnetic resonance, imputation, t-test, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155768 | SCR_002397 | 2026-09-19 12:57:45 | 0 | ||||||||
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Measure Projection Toolbox Resource Report Resource Website 1+ mentions |
Measure Projection Toolbox (RRID:SCR_002429) | MPT | software resource, software toolkit | This toolbox is an EEGLAB plugin for performing Measure Projection Analysis. Measure Projection Analysis (MPA) is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component (IC) clustering issues by abandoning the notion of distinct IC clusters. Instead, it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects and/or sessions as quantified by the values of various EEG measures. Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences. | reusable library, eeg, meg, electrocorticography, matlab, statistical operation, surrogate data analysis, visualization, measure projection analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Swartz Center for Computational Neuroscience |
Free, Available for download, Freely available | nlx_155809 | http://www.nitrc.org/projects/measure_project | SCR_002429 | Measure Projection Toolbox (MPT) | 2026-09-19 12:57:45 | 3 | ||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software application, software resource, software toolkit | A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished. | reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: neurodebian |
Free, Available for download, Freely available | nlx_155536 | http://www.nitrc.org/projects/cmtk, https://sources.debian.org/src/cmtk/ | SCR_002234 | Computational Morphometry Toolkit (CMTK) | 2026-09-19 12:57:44 | 38 | ||||||
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RFT FDR Resource Report Resource Website |
RFT FDR (RRID:SCR_002533) | RFT_FDR | software application, software resource | So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171). | console (text based), gnome, kde, matlab, mgh/mgz, modeling, magnetic resonance, os independent, rendering, statistical operation, surface analysis, surface rendering, thickness, visualization, random field theory |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155938 | SCR_002533 | RFT-FDR, RFT FDR | 2026-09-19 12:57:45 | 0 | |||||||
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NIRx2nirs: A NIRx to .nirs data converter Resource Report Resource Website 1+ mentions |
NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) | NIRx2nirs | software application, software resource | A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge. | hardware, nirs, fnir, optical imaging, optical imaging, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Homer2 |
Free, Available for download, Freely available | nlx_155887 | SCR_002492 | 2026-09-19 12:57:45 | 1 | ||||||||
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MBF BioScience: Stereo Investigator Resource Report Resource Website 100+ mentions |
MBF BioScience: Stereo Investigator (RRID:SCR_002526) | instrument resource, software resource | Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. | stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
Restricted | SciRes_000114, SCR_024705, SCR_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | Stereo Investigator system | 2026-09-19 12:57:45 | 162 | |||||||
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Slicer3 Example Modules Resource Report Resource Website |
Slicer3 Example Modules (RRID:SCR_002559) | Slicer3 Example Modules | software application, software development tool, software resource | Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions | analyze, c++, console (text based), computed tomography, dicom, linux, macos, microsoft, magnetic resonance, nifti, pet, spect, platform or development environment, posix/unix-like, win32 (ms windows), windows, windows nt/2000, windows vista |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center |
Free, Available for download, Freely available | nlx_155965 | SCR_002559 | 2026-09-19 12:57:45 | 0 | ||||||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software application, software resource, software toolkit | A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics. | analyze, c, matlab, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows, parametric surface model, spherical harmonics, 3d, shape modeling, analysis, morphometry |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University School of Medicine; Indiana; USA |
NIBIB R03EB008674-01 | Free, Available for download, Freely available | nlx_155952 | http://www.nitrc.org/projects/spharm-mat | SCR_002545 | 2026-09-19 12:57:45 | 2 | ||||||
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cortex Resource Report Resource Website 100+ mentions |
cortex (RRID:SCR_002467) | cortex | software application, software resource | Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clinical neuroinformatics, mgh/mgz, magnetic resonance, r, surface analysis, thickness, mri, cortical thickness, morphometry, neuroimaging, power analysis, study design, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: bio.tools is listed by: Debian has parent organization: Brain Research Institute |
PMID:22807270 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155842, biotools:cortex | http://brain.org.au/software/cortex/power, http://www.nitrc.org/projects/cortex, https://bio.tools/cortex | SCR_002467 | Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies | 2026-09-19 12:57:45 | 374 | |||||
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Diffusion Tractography with Kalman Filter Resource Report Resource Website |
Diffusion Tractography with Kalman Filter (RRID:SCR_002585) | Diffusion Tractography with Kalman Filter | software application, software resource | Software framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation. The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application. | c++, diffusion mr fiber tracking, fiber tracking, microsoft, magnetic resonance, nrrd, posix/unix-like, tractography, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:19694258 | Free, Available for download, Freely available | nlx_155990 | SCR_002585 | Tractography with Unscented Kalman Filter | 2026-09-19 12:57:45 | 0 |
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