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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Brede Wiki Resource Report Resource Website |
Brede Wiki (RRID:SCR_001411) | data or information resource, narrative resource, wiki | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format. | neuroinformatics, neuroscience, functional neuroimaging, molecular neuroimaging, fmri, mri, talairach, brain region, data sharing, mediawiki, sql |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Toolbox is related to: Brede Database has parent organization: Technical University of Denmark; Lyngby; Denmark |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-08130 | http://www.nitrc.org/projects/bredewiki | SCR_001411 | Brede Wiki - a neuroinformatics wiki | 2026-02-12 09:43:09 | 0 | |||||||
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MRI Studio Resource Report Resource Website 100+ mentions |
MRI Studio (RRID:SCR_001398) | software resource, software application, data processing software, data visualization software, image processing software, image analysis software | An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration | tensor calculation, color mapping, fiber tracking, 3d visualization, dti, image registration, mri, diffusion mr fiber tracking, microsoft, c++, analyze |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion Tensor Imaging ToolKit has parent organization: Johns Hopkins University; Maryland; USA works with: UManitoba - JHU Functionally Defined Human White Matter Atlas |
NCRR ; Biomedical Informatics Research Network ; NIBIB |
Free, Freely Available | nif-0000-00291 | http://www.nitrc.org/projects/mri_studio | SCR_001398 | dtiStudio, DTI Studio | 2026-02-12 09:43:09 | 165 | ||||||
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Atlas3D Resource Report Resource Website 10+ mentions |
Atlas3D (RRID:SCR_001808) | software resource, atlas, software application, data processing software, data or information resource, data visualization software | A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images. | analysis, brain, histological, mouse, rat, slicing, structure, 3d, tomographic, visualization, neuroimaging, image, magnetic resonance, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Oslo; Oslo; Norway |
Research Council of Norway ; NIH ; NIBIB R01-EB00790; NCRR U24-RR021382 |
Free, Freely available | nif-0000-10373 | http://www.nitrc.org/projects/incf_atlas3d | SCR_001808 | Neural Systems and Graphics Computing Laboratory: Atlas3D Software, NeSys Atlas3D | 2026-02-12 09:43:14 | 17 | ||||||
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PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | software toolkit, software resource, software application, data analysis software, data processing software | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/ https://www.cog-genomics.org/plink/1.9/general_usage#cite https://sources.debian.org/src/plink/ |
http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-02-12 09:43:13 | 15344 | |||||
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NIDAG: Neuroimaging Data Access Group Resource Report Resource Website |
NIDAG: Neuroimaging Data Access Group (RRID:SCR_001674) | NIDAG | international standard specification, standard specification, narrative resource, data or information resource, knowledge environment | An international working group dedicated to improving access to neuroimaging results in a free and open-access manner. It seeks to establish a universal coordinate database, including both past papers and future studies. Their current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, they hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships. They are interested in hearing from people who might be willing to contribute to their projects, particularly those with programming experience. The number of published neuroimaging studies is increasing rapidly and it is not feasible to read them all. If a computer database could store key information from published fMRI papers and make that information easier to search or share, this would have substantial benefits for the neuroimaging community. Projects like AMAT, Brainmap, Brede and SumsDB have started to tackle this problem. NIDAG wants to formalize and improve these databases so that they meet the needs of the neuroimaging community. Formal meta-analysis of published data is a valuable way to assess the consistency and reliability of experimental results. A database of neuroimaging results would facilitate meta-analyses, in conjunction with tools like GingerALE and Multi-level Kernel Density Analysis. | fmri, database, neuroimaging, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: AMAT |
Free, Freely Available | nif-0000-10161 | http://www.nitrc.org/projects/nidag | SCR_001674 | Neuroimaging Data Access Group | 2026-02-12 09:43:12 | 0 | ||||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | software resource, software application, image analysis software, data processing software, data visualization software | Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR U24 RR021382; NINDS R01 NS052585; NCRR RR014075 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/ http://www.nitrc.org/projects/freesurfer http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall |
SCR_001847 | 2026-02-12 09:43:15 | 11817 | |||||
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Virtual brain Resource Report Resource Website 10+ mentions |
Virtual brain (RRID:SCR_002249) | tvb | simulation software, software application, software resource | Simulation software for modeling the entire human brain by combining structural and functional data from empirical neuroimaging data. It can generate local field potentials, EEG, MEG and fMRI BOLD data based on neural mass models. The user can also modify the model parameters to match clinical conditions from focal lesions or degenerative disorders. | dti, simulation, modeling, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Toronto; Ontario; Canada |
James S. McDonnell Foundation | PMID:23442172 PMID:23774395 |
Free, Freely available | nlx_155567 | http://www.nitrc.org/projects/tvb | SCR_002249 | thevirtualbrain.org, The Virtual Brain, thevirtualbrain | 2026-02-12 09:43:19 | 39 | ||||
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VoxBo Resource Report Resource Website 10+ mentions |
VoxBo (RRID:SCR_002166) | VoxBo | software resource, software application, data processing software, image processing software, image analysis software | Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more. | fmri, neuroimaging, brain, functional, statistical, volume, preprocessing, analysis, display, format conversion, linear, three dimensional display, workflow, lesion, analyze, c++, console (text based), dicom, image display, linux, macos, microsoft, magnetic resonance, nifti, no input/output (daemon), overlap metrics, posix/unix-like, quantification, regression, resampling, sinc function interpolation, spatial transformation, statistical operation, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian has parent organization: neurodebian |
NIDA R01DA014418; NIMH R01MH073529 |
PMID:22348882 | Free, Available for download, Freely available | nif-0000-00353 | https://sources.debian.org/src/voxbo/ https://github.com/kimberg/voxbo |
http://www.voxbo.org/ | SCR_002166 | 2026-02-12 09:43:18 | 13 | ||||
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Medical Image Visualization and Analysis Resource Report Resource Website 1+ mentions |
Medical Image Visualization and Analysis (RRID:SCR_002315) | MIVA | software resource, atlas, software application, data processing software, data or information resource, image analysis software | Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator. | magnetic resonance, fmri, graphical interface, display, segment, align, manipulate, blend, registration, alignment, region of interst, volume of interest, 3d geometry tool, 3d |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Worcester Polytechnic Institute; Massachusetts; USA |
BSD License | nlx_155664 | SCR_002315 | 2026-02-12 09:43:20 | 8 | ||||||||
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MriWatcher Resource Report Resource Website 1+ mentions |
MriWatcher (RRID:SCR_002318) | MriWatcher | software application, data processing software, software resource, data visualization software | This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155667 | SCR_002318 | 2026-02-12 09:43:20 | 2 | ||||||||
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MGDM: Multi Geometric Deformable Model Resource Report Resource Website |
MGDM: Multi Geometric Deformable Model (RRID:SCR_002311) | MGDM | software resource, segmentation software, software application, data processing software, image analysis software | An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming. | algorithm, reusable library, computed tomography, java, matlab, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155658 | SCR_002311 | Multi Geometric Deformable Model | 2026-02-12 09:43:20 | 0 | |||||||
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BRAINSFit Resource Report Resource Website 10+ mentions |
BRAINSFit (RRID:SCR_002340) | BRAINSFit | software resource, software application, registration software, data processing software, image analysis software | A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3 | affine warp, analyze, c++, console (text based), dicom, image-to-image, intermodal, intersubject, linear warp, macos, microsoft, magnetic resonance, nifti, os independent, posix/unix-like, registration, spatial transformation, warping, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155701 | http://www.nitrc.org/projects/multimodereg | SCR_002340 | 2026-02-12 09:43:21 | 20 | |||||||
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S-rep Fitting Statistics and Segmentation Resource Report Resource Website |
S-rep Fitting Statistics and Segmentation (RRID:SCR_002540) | S-rep Fitting Statistics and Segmentation | software resource, segmentation software, software application, data processing software, image analysis software | Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed. | computational neuroscience, computed tomography, domain independent, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155948 | SCR_002540 | 2026-02-12 09:43:23 | 0 | ||||||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | software resource, software application, data analysis software, data processing software | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-02-12 09:43:23 | 17 | ||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | data or information resource, narrative resource, discussion, knowledge environment | Project to discuss, debate, develop and deploy ontological practices for the fMRI community. | community, ontology, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155943 | SCR_002536 | 2026-02-12 09:43:23 | 0 | ||||||||
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MCML and CONV Resource Report Resource Website |
MCML and CONV (RRID:SCR_002419) | MCML, MCML & CONV, CONV | simulation software, software application, software resource | MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications. | optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Oregon Health and Science University; Oregon; USA |
PMID:9421660 PMID:19256707 |
Free, Available for download, Freely available | nlx_155791 | http://www.nitrc.org/projects/mcml | SCR_002419 | Monte Carlo for Multi-Layered media | 2026-02-12 09:43:22 | 0 | |||||
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Rodent Cortical Thickness Analysis Resource Report Resource Website |
Rodent Cortical Thickness Analysis (RRID:SCR_002539) | software resource, software application, data processing software, image processing software, image analysis software | An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling | microscopy, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155946 | http://www.nitrc.org/projects/rodentthickness | SCR_002539 | RodentThickness | 2026-02-12 09:43:23 | 0 | |||||||
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Rodent Brain Extraction Tool Resource Report Resource Website |
Rodent Brain Extraction Tool (RRID:SCR_002538) | rBET | software application, image processing software, software resource, data processing software | A modified version of the Brain Extraction Tool (BET) that can process rodent brains. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: King's College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_155945 | http://www.nitrc.org/projects/rbet | SCR_002538 | 2026-02-12 09:43:23 | 0 | |||||||
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NPTK Resource Report Resource Website |
NPTK (RRID:SCR_002496) | NPTK | software resource, software application, registration software, data processing software, 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 | 2026-02-12 09:43:23 | 0 | ||||||||
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NITRC Enhanced Services Resource Report Resource Website |
NITRC Enhanced Services (RRID:SCR_002494) | NITRC Enhanced Services | data or information resource, portal, community building portal, service resource | 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 | 2026-02-12 09:43:23 | 0 |
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