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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Papaya Resource Report Resource Website 1+ mentions |
Papaya (RRID:SCR_014188) | software resource, source code | A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+). | source code, javascript, medical research, image viewer | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | https://github.com/rii-mango/Papaya/ | SCR_014188 | 2026-02-14 02:07:56 | 5 | |||||||||
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Efficient Permutation Testing Resource Report Resource Website |
Efficient Permutation Testing (RRID:SCR_014104) | software resource, source code | A Matlab implementation for efficient permutation testing by using matrix completion. | permutation, nueroimaging, source code, fast, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Wisconsin Partnership Fund ; NIA R01 AG040396; NSF CAREER 1252725; NSF RI 1116584; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; Veterans Administration Merit Review I01CX000165 |
Available for download, Acknowledgement requested | http://pages.cs.wisc.edu/~vamsi/pt_fast.html | SCR_014104 | Speeding Up Permutation Testing in Neuroimaging | 2026-02-14 02:08:23 | 0 | |||||||
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YMDTI: Diffusion Tensor Images of Healthy Young Males Resource Report Resource Website |
YMDTI: Diffusion Tensor Images of Healthy Young Males (RRID:SCR_014183) | YMDTI | data or information resource, data set | A dataset which contains diffusion tensor images of 93 healthy, young male subjects. | data set, diffusion tensor image, young male subject | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014183 | Diffusion Tensor Images of Healthy Young Males | 2026-02-14 02:08:23 | 0 | ||||||||
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Epilepsy T1 and Hippocampal Segmentation Datasets Resource Report Resource Website |
Epilepsy T1 and Hippocampal Segmentation Datasets (RRID:SCR_014926) | data or information resource, data set | Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site. | hippocampus, t1, dataset, skull stripped, mri, segmented hippocampus, epilepsy, temporal lobe epilepsy, tle | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_014926 | 2026-02-14 02:07:58 | 0 | ||||||||||
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dinifti Resource Report Resource Website 1+ mentions |
dinifti (RRID:SCR_000303) | dinifti | software resource, software application | 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 | 2026-02-14 02:06:28 | 2 | ||||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software resource, software application | 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 | 2026-02-14 02:06:58 | 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 | systems interoperability software, software resource, software application | 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 | 2026-02-14 02:06:59 | 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 | 2026-02-14 02:07:01 | 0 | ||||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software resource, software toolkit, software application | 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) | 2026-02-14 02:07:01 | 33 | ||||||
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RFT FDR Resource Report Resource Website |
RFT FDR (RRID:SCR_002533) | RFT_FDR | software resource, software application | 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 | 2026-02-14 02:07:01 | 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 resource, software application | 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 | 2026-02-14 02:06:55 | 1 | ||||||||
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Stereo Investigator Resource Report Resource Website 100+ mentions |
Stereo Investigator (RRID:SCR_002526) | software resource, instrument 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_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | Stereo Investigator system | 2026-02-14 02:06:42 | 145 | |||||||
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Slicer3 Example Modules Resource Report Resource Website |
Slicer3 Example Modules (RRID:SCR_002559) | Slicer3 Example Modules | software resource, software application, software development tool | 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 | 2026-02-14 02:06:33 | 0 | ||||||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software resource, software toolkit, software application | 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 | 2026-02-14 02:06:55 | 2 | ||||||
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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) | 2026-02-14 02:06:42 | 3 | ||||||
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cortex Resource Report Resource Website 100+ mentions |
cortex (RRID:SCR_002467) | cortex | software resource, software application | 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 | 2026-02-14 02:06:42 | 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 resource, software application | 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 | 2026-02-14 02:06:42 | 0 | ||||||
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shapeAnalysisMANCOVA - SPHARM tools Resource Report Resource Website |
shapeAnalysisMANCOVA - SPHARM tools (RRID:SCR_002578) | shapeAnalysisMANCOVA | software resource, software application | shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description (SPHARM) as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance (MANCOVA). Here, the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts, and to account for independent variables, a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues. Details of the methods can be found in its Insight Journal publication: http://hdl.handle.net/10380/3124 | c++, console (text based), macos, magnetic resonance, posix/unix-like, shape analysis, shape decomposition, spherical harmonics, statistical operation, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Free, Available for download, Freely available | nlx_155980 | SCR_002578 | 2026-02-14 02:06:33 | 0 | ||||||||
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pydicom Resource Report Resource Website 50+ mentions |
pydicom (RRID:SCR_002573) | pydicom | software resource, software toolkit | Software Python package for working with DICOM files, made for inspecting and modifying DICOM data in an easy pythonic way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements. | reusable library, console (text based), dicom, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian |
Free, Available for download, Freely available | nlx_155976 | http://www.nitrc.org/projects/pydicom https://sources.debian.org/src/python3-pydicom/ |
http://pydicom.googlecode.com | SCR_002573 | 2026-02-14 02:06:42 | 90 | ||||||
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Net Station EEG Software Resource Report Resource Website 50+ mentions |
Net Station EEG Software (RRID:SCR_002453) | Net Station | software resource, software application, commercial organization | A complete software package for working with electroencephalography (EEG) and event-related potential (ERP) data. You can acquire, review, analyze, and now ?see? your participant with synchronized video. Net Station also offers specialized tools and workflow options for both clinical and research applications, allows you to save different combinations of view settings (called workspaces) and helps with your reporting requirements by letting you set up and print custom cover pages. For more specialized work, Net Station also provides an optional electrical source estimation module (GeoSource) and an optional sensor location digitizer (Geodesic Photogrammetry System). | animation, eeg, meg, electrocorticography, event related potential, format conversion, spectral analysis, temporal transformation, time domain analysis, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: Net Station API |
Restricted | nlx_155825 | SCR_002453 | Netstation | 2026-02-14 02:07:01 | 68 |
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