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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NPTK Resource Report Resource Website |
NPTK (RRID:SCR_002496) | NPTK | data processing software, software application, registration software, software resource, image analysis software | Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. | analyze, artifact removal, c++, image-to-image, intermodal, linux, macos, microsoft, magnetic resonance, nifti, nonlinear warp, posix/unix-like, registration, spatial transformation, warping, windows, windows xp, fmri, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155893 | SCR_002496 | 2026-02-14 02:00:25 | 0 | ||||||||
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NITRC Enhanced Services Resource Report Resource Website |
NITRC Enhanced Services (RRID:SCR_002494) | NITRC Enhanced Services | service resource, data or information resource, portal, community building portal | Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data. | data, database, data resource, dicom, domain independent, information resource, nifti, platform or development environment, software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NITRC Computational Environment is related to: NITRC-IR has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155890 | SCR_002494 | 2026-02-14 02:00:17 | 0 | ||||||||
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NiBabel Resource Report Resource Website 100+ mentions |
NiBabel (RRID:SCR_002498) | NiBabel | software resource | A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI. | magnetic resonance, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PyNIfTI is related to: MNE software has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155896 | http://www.nitrc.org/projects/nibabel | SCR_002498 | NIPY File IO | 2026-02-14 02:00:25 | 122 | ||||||
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NIRAL Utilities Resource Report Resource Website |
NIRAL Utilities (RRID:SCR_002490) | NIRAL Utilities | data processing software, software application, image processing software, software resource, image analysis software | Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images | analyze, c++, console (text based), linux, macos, microsoft, magnetic resonance, nrrd, posix/unix-like |
is used by: NeoSegPipeline is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Free, Freely avaialble | nlx_155884 | SCR_002490 | 2026-02-14 02:00:24 | 0 | ||||||||
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Pythagorean Displacement and Motion Regressors Resource Report Resource Website 1+ mentions |
Pythagorean Displacement and Motion Regressors (RRID:SCR_002525) | Pythagorean Displacement and Motion Regressors | software resource | Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment. | algorithm, magnetic resonance, matlab, pythagorean theorem, head, motion, position, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155931 | SCR_002525 | 2026-02-14 02:00:26 | 5 | ||||||||
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PySurfer Resource Report Resource Website 10+ mentions |
PySurfer (RRID:SCR_002524) | PySurfer | data visualization software, data processing software, software library, software toolkit, software application, software resource | Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155930 | http://www.nitrc.org/projects/pysurfer https://sources.debian.org/src/python3-surfer/ |
SCR_002524 | 2026-02-14 02:00:25 | 29 | |||||||
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Spanish Resting State Network Resource Report Resource Website |
Spanish Resting State Network (RRID:SCR_002562) | SRSN | data or information resource, portal, community building portal | Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.) | microsoft word document, magnetic resonance, nifti, pdf, spanish |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 1000 Functional Connectomes Project |
Free | nlx_155968 | SCR_002562 | 2026-02-14 02:00:25 | 0 | ||||||||
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Slice:Drop Resource Report Resource Website 1+ mentions |
Slice:Drop (RRID:SCR_002557) | Slice:Drop | analysis service resource, production service resource, source code, service resource, software resource | A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ). | ascii, clinical neuroinformatics, computed tomography, dicom, javascript, mgh/mgz, magnetic resonance, nifti, nrrd, medical imaging, 3d, visualization, rendering | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155964 | http://www.nitrc.org/projects/slicedrop | SCR_002557 | 2026-02-14 02:00:27 | 5 | |||||||
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Sleuth Resource Report Resource Website 100+ mentions |
Sleuth (RRID:SCR_002555) | data visualization software, data processing software, web application, data analysis software, software application, software resource | Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space. | brain map database, data visualization, neuroscience literature, talairach space, search software, meta-data analysis |
uses: MNI brain and the Talairach atlas uses: MNI brain and the Talairach atlas is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: brainmap.org |
Public, Account required, Available for download | nlx_155963 | http://www.nitrc.org/projects/brainmap | SCR_002555 | Sleuth Version 2.4 | 2026-02-14 02:00:25 | 204 | |||||||
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Signed Differential Mapping Resource Report Resource Website 100+ mentions |
Signed Differential Mapping (RRID:SCR_002554) | SDM | software resource | Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera). | magnetic resonance, pet, spect, fmri, vbm, meta-analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155962 | http://www.nitrc.org/projects/sdm | SCR_002554 | 2026-02-14 02:00:27 | 150 | |||||||
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WFU Biological Parametric Mapping Toolbox Resource Report Resource Website 1+ mentions |
WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) | WFU_BPM, WFU BPM | data processing software, software toolkit, software application, software resource, image analysis software | Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher | analyze, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, statistical operation, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Wake Forest School of Medicine; North Carolina; USA |
Human Brain Project ; NIBIB 1R01EB004673 |
PMID:17070709 | Free, Available for download, Freely available | nlx_156016 | http://www.nitrc.org/projects/wfu_bpm | SCR_002613 | BPM - Integrated Tool for Biological Parametric Mapping, WFU Biological Parametric Mapping, BPM toolbox, BPM | 2026-02-14 02:00:28 | 4 | ||||
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peak nii Resource Report Resource Website 1+ mentions |
peak nii (RRID:SCR_002572) | peak_nii | data processing software, software toolkit, software application, image processing software, software resource | Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command. | magnetic resonance, pet, spect | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Personal License | nlx_155975 | SCR_002572 | peak_nii: Statistical image clustering peak detection and data extraction, peak nii | 2026-02-14 02:00:27 | 7 | |||||||
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Vaa3D Resource Report Resource Website 100+ mentions |
Vaa3D (RRID:SCR_002609) | Vaa3D, Vaa3D-Neuron | data visualization software, data processing software, data management software, software toolkit, software application, software resource, image analysis software | A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools. | reusable library, atlas application, c, c++, cygwin, fiber tracking, gnome, image display, kde, linux, macos, microsoft, magnetic resonance, neuronal characterization, development environment, position, posix/unix-like, quantification, registration, rendering, resampling, segmentation, shape analysis, spatial transformation, surface analysis, tractography, visualization, volumetric analysis, warping, win32 (ms windows), windows, windows 95/98/2000, windows nt/2000, windows vista, windows xp, 3d neuron reconstruction, 3d, neuron, reconstruction, microscopy |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Insight Segmentation and Registration Toolkit has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | Free, Available for download, Freely available | nlx_156012 | http://www.nitrc.org/projects/v3d | SCR_002609 | V3D, Vaa3D: A Swiss army knife for bioimage visualization & analysis, V3D-Neuron, Vaa3D: A Swiss army knife for bioimage visualization and analysis, 3D Visualization-Assisted Analysis, Vaa3D and Vaa3D-Neuron | 2026-02-14 02:00:18 | 157 | ||||
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Triangle BioSystems Resource Report Resource Website 10+ mentions |
Triangle BioSystems (RRID:SCR_002603) | TBSI | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software | computational neuroscience, eeg, eeg, meg, electrocorticography, hardware, other software resource, physiological recording, software | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156006 | http://www.nitrc.org/projects/tbsi | SCR_002603 | Triangle BioSystems International | 2026-02-14 02:00:28 | 11 | ||||||
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TractoR: Tractography with R Resource Report Resource Website 10+ mentions |
TractoR: Tractography with R (RRID:SCR_002602) | TractoR | software resource, data visualization software, data processing software, software application | Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R. | analyze, atlas application, c, dicom, linux, macos, modeling, magnetic resonance, nifti, other unix-like, posix/unix-like, quantification, r, segmentation, sh, bash, statistical operation, tractography, unix shell, visualization, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_156005 | http://www.nitrc.org/projects/tractor | SCR_002602 | Tractography with R | 2026-02-14 02:00:17 | 28 | ||||||
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TetraMetrix Resource Report Resource Website 1+ mentions |
TetraMetrix (RRID:SCR_002601) | TetraMetrix | software resource | An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left. | magnetic resonance, 3d, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
Free, Available for download, Freely available | nlx_156004 | SCR_002601 | 2026-02-14 02:00:27 | 1 | ||||||||
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Template Image Processing Library Resource Report Resource Website |
Template Image Processing Library (RRID:SCR_002600) | TIPL | data processing software, software library, software toolkit, software application, image processing software, software resource, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an easy-to-use and also ready-to-use library. The code is template-based, and only header files are needed to be included to the source code. This library provides the following functions: # DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w) # numerical: add, multiply, gradient. # interpolation: linear, gaussian radial basis # filters: mean, gaussian, laplacian, sobel, anisotropic diffusion # morphological processing: erosion, expansion, opening, closing # template-based Fourier transform # linear coregistration: rigid body, affine transform, least square fit, mutual information # nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM) | reusable library, analyze, c++, dicom, format conversion, magnetic resonance, nifti, os independent, segmentation, spatial transformation, visualization, win32 (ms windows) |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156003 | http://www.nitrc.org/projects/tipl | SCR_002600 | 2026-02-14 02:00:25 | 0 | |||||||
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TurtleSeg Resource Report Resource Website 1+ mentions |
TurtleSeg (RRID:SCR_002605) | TurtleSeg | data processing software, software application, segmentation software, software resource, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process. | analyze, c++, computed tomography, dicom, intensity contour, microsoft, minc, magnetic resonance, nifti, segmentation, win32 (ms windows), windows, windows nt/2000, windows vista, windows xp | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156008 | http://www.nitrc.org/projects/turtleseg | SCR_002605 | TurtleSeg - Interactive 3D Image Segmentation Software | 2026-02-14 02:00:25 | 6 | ||||||
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PHYCAA+: adaptive physiological noise correction for BOLD fMRI Resource Report Resource Website 1+ mentions |
PHYCAA+: adaptive physiological noise correction for BOLD fMRI (RRID:SCR_002514) | PHYCAA+ | image processing software, software resource, data processing software, software application | Software algorithm that automatically estimates and removes physiological noise in BOLD fMRI data, including the effects of heartbeat and respiration. This algorithm (1) masks out high-variance CSF and vascular tracts that may otherwise confound analyses, and (2) regresses out noise timeseries in grey matter tissue, using an adaptive multivariate component decomposition (Canonical Autocorrelations Analysis). PHYCAA+ is an efficient, automated procedure that does NOT require external measures of physiology, nor does it require the user to manually identify noise components. Based on the peer-reviewed article: Churchill & Strother (2013). PHYCAA+: An Optimized, Adaptive Procedure for Measuring and Controlling Physiological Noise in BOLD fMRI. NeuroImage 82: 306-325 | algorithm, matlab, magnetic resonance, nifti, os independent, fmri, bold, bold fmri, multivariate, physiological noise |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Toronto; Ontario; Canada |
PMID:23727534 | GNU Lesser General Public License | nlx_155913 | SCR_002514 | 2026-02-14 02:00:26 | 7 | |||||||
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PennCNV Resource Report Resource Website 100+ mentions |
PennCNV (RRID:SCR_002518) | PennCNV | software resource | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm. | imaging genomics, copy number variation, snp, genotyping array, array, oligonucleotide, hidden markov model, genotype, genome |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VegaMC is related to: OpenBioinformatics.org has parent organization: University of Pennsylvania; Philadelphia; USA |
NIMH MH604687 | PMID:17921354 | Free | OMICS_00729, nlx_155921 | http://www.openbioinformatics.org/penncnv/ |
http://www.neurogenome.org/cnv/penncnv | SCR_002518 | PennCNV: copy number variation detection | 2026-02-14 02:00:26 | 349 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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