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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GIMIAS Resource Report Resource Website 1+ mentions |
GIMIAS (RRID:SCR_009545) | GIMIAS | software application, software resource | A workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology. | analyze, c++, clinical neuroinformatics, dicom, microsoft, magnetic resonance, nifti, platform, posix/unix-like, software, win32 (ms windows), windows, computing, simulation, visualization, processing, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Pompeu Fabra University; Barcelona; Spain |
BSD License | nlx_155762 | http://www.nitrc.org/projects/gimias_fw | http://www.gimias.net/ | SCR_009545 | Graphical Interface for Medical Image Analysis and Simulation | 2026-08-04 09:42:25 | 6 | |||||
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DICOMConvert Resource Report Resource Website |
DICOMConvert (RRID:SCR_014100) | software application, standalone software, software resource | A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd). | standalone software, dicom, image converter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
Center for Infectious Disease Imaging ; NIAID ; NIBIB |
Available for download | SCR_014100 | Dicom Converter | 2026-08-04 09:43:20 | 0 | ||||||||
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Notion ResearchPACS Resource Report Resource Website |
Notion ResearchPACS (RRID:SCR_014154) | software application, standalone software, software resource | Standalone software designed to be used by radiology researchers for storage and anonymization of research images. | standalone software, radiology, storage, research image, anonymization, pacs | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014154 | 2026-08-04 09:43:21 | 0 | ||||||||||
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Neurodocker Resource Report Resource Website 1+ mentions |
Neurodocker (RRID:SCR_017426) | software application, software resource | Software tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12. | Generate, Dockerfile, singularity, recipe, neuroimaging, command-line, interface, minify, container | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | https://www.nitrc.org/projects/neurodocker/ | SCR_017426 | 2026-08-04 09:44:10 | 4 | |||||||||
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LONI Debabeler Resource Report Resource Website |
LONI Debabeler (RRID:SCR_001160) | Debabeler | software application, software resource | Software to manage the conversion of imaging data from one file format and convention to another. It consists of a graphical user interface to visually program the translations, and a data translation engine to read, sort and translate the input files, and write the output files to disk. The data translation engine: (1) Reads metadata from a set of image files on disk to identify the source that produced each file; (2) Groups the image files into user-defined collections using image metadata values; (3) Translates each image file collection by reading metadata and pixel data and mapping the data into the appropriate output file format through a programmable set of connected modules. The Debabeler uses the Java Image I/O Plugin Architecture to read and write a wide variety of common medical image file formats, including ANALYZE, MINC, and most variations of DICOM. | workflow, java, analyze, dicom, minc, nifti-1, neuroimaging, file format, translation, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
PMID:15670695 | Free, Available for download, Freely available | nif-0000-00321 | http://www.nitrc.org/projects/debabeler | SCR_001160 | 2026-08-04 09:40:19 | 0 | |||||
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MEG Tools Resource Report Resource Website |
MEG Tools (RRID:SCR_000661) | MEG Tools | software application, software resource | A software program for source imaging Magnetoencephalographic data. Now MEG tools has added Imaged Coherence mapping, Talairach and MNI coordinates, Grainger Causality. MEG Tools also includes MR-FOCUSS, ECD, Beamformers and many other useful MEG tools. This is a Matlab-based software module that is used to image MEG data onto a patient's MRI. This software imports all MEG manufacture's data (4D-Neuroimaging/BTi, CTF and Neuromag/Elekta). | eeg, meg, electrocorticography, image reconstruction, matlab, microsoft, win32 (ms windows), mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155792 | http://www.nitrc.org/projects/meg-tools | SCR_000661 | 2026-08-04 09:40:11 | 0 | |||||||
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PsychoPy Resource Report Resource Website 1000+ mentions |
PsychoPy (RRID:SCR_006571) | PsychoPy | software application, software resource | Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime. | console (text based), experimental control, freebsd, linux, macos, microsoft, magnetic resonance, posix/unix-like, python, win32 (ms windows), windows, neuroscience, psychology, psychophysics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Nottingham; Nottingham; United Kingdom |
PMID:17254636 PMID:19198666 |
GNU General Public License | nlx_155928 | http://www.nitrc.org/projects/psychopy, https://sources.debian.org/src/psychopy/ | SCR_006571 | PsychoPy - Psychology software in Python | 2026-08-04 09:41:37 | 1975 | |||||
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Spatial Analysis 3D Resource Report Resource Website |
Spatial Analysis 3D (RRID:SCR_002563) | SA3D | software application, software resource | A user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes. | eeg, meg, electrocorticography, matlab, modeling, magnetic resonance, position, quantification, simulation, statistical operation, cell, microscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Santa Barbara; California; USA |
NIMH MH-069997; NEI EY-011087 |
PMID:18644136 | Free, Available for download, Freely available | nlx_155969 | http://www.nitrc.org/projects/sa3d | SCR_002563 | 2026-08-04 09:40:40 | 0 | |||||
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ShapeComplexAtlas Resource Report Resource Website |
ShapeComplexAtlas (RRID:SCR_002553) | ShapeComplexAtlas | software application, software resource | A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012 | atlas application, matlab, magnetic resonance, mri, shape complex atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NSF RI-IIS 0954032; NSF IIS 1143963 |
PMID:22305953 PMID:20879384 |
Free, Available for download, Freely available | nlx_155960 | http://www.nitrc.org/projects/shapecomplex | SCR_002553 | 2026-08-04 09:40:42 | 0 | |||||
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SPHARM-PDM Toolbox Resource Report Resource Website |
SPHARM-PDM Toolbox (RRID:SCR_002546) | SPHARM-PDM Toolbox | software application, software resource | Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures. | analyze, c++, console (text based), macos, microsoft, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: National Alliance for Medical Image Computing has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:24027625 | Free, Available for download, Freely available | nlx_155953 | http://www.nitrc.org/projects/spharm-pdm | SCR_002546 | UNC SPHARM-PDM, SPHARM-PDM UNC Toolbox | 2026-08-04 09:40:40 | 0 | |||||
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Working Memory Trainer Resource Report Resource Website |
Working Memory Trainer (RRID:SCR_002617) | WM Trainer | software application, software resource | A stand-alone axecutable under all main Windows OS for training the working memory. The WM Trainer looks and behaves a little bit like a video-game and has been specifically conceived for children attending the primary school. However, it can be used purposefully by people of any age, including adult and elderly. This application features highest graphic quality, a powerful adaptive engine for the difficulty level, a database of users and statistical tools to evaluate the progress. Currently English, French and Italian are supported, but any language can be easily supported. | clinical neuroinformatics, memory, french, italian | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_156022 | SCR_002617 | 2026-08-04 09:40:41 | 0 | ||||||||
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scikit-learn Resource Report Resource Website 10000+ mentions |
scikit-learn (RRID:SCR_002577) | scikit-learn | software application, software resource | scikit-learn: machine learning in Python | algorithm, discriminant analysis, independent component analysis, linear, macos, microsoft, modeling, magnetic resonance, nonlinear, posix/unix-like, principal component analysis, python, regression, statistical operation, windows, data mining, data analysis, classification, clustering, dimensionality reduction, model selection, preprocessing, machine learning | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:24600388 | Free, Available for download, Freely available | nlx_155979 | http://www.nitrc.org/projects/scikit-learn | SCR_002577 | scikit-learn: machine learning in Python | 2026-08-04 09:40:41 | 12132 | |||||
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VR Worlds 2 Resource Report Resource Website |
VR Worlds 2 (RRID:SCR_002608) | VR Worlds 2 | software application, commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. NOTE: VR Worlds 2 is no longer available as a standalone software. Software application designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2?s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including: * Residential/Urban Area * Hotel Lobby * Medical Office * Grocery Store * Neighborhood for drug and alcohol cue extinction treatment (featured on GMA, motion capture process) * Casino for gambling addiction research (featured on Canadian Discovery Channel) * Driving simulation for mild cognitive impairment research * Phobia scenarios * Spatial navigation mazes | eeg, meg, electrocorticography, experimental control, microsoft, magnetic resonance, win32 (ms windows), windows, windows vista, windows xp, neurobehavior, virtual environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156011 | http://www.nitrc.org/projects/vr2 | SCR_002608 | 2026-08-04 09:40:41 | 0 | |||||||
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LONI Provenance Editor Resource Report Resource Website |
LONI Provenance Editor (RRID:SCR_002483) | LONI Provenance Editor | software application, software resource | A self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information. | computed tomography, magnetic resonance, pet, spect, provenance, image header |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
PMID:20927408 PMID:21791102 |
Free, Freely avaialble | nlx_155876 | http://www.nitrc.org/projects/provenance | SCR_002483 | 2026-08-04 09:40:39 | 0 | ||||||
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TARQUIN Resource Report Resource Website 50+ mentions |
TARQUIN (RRID:SCR_002598) | TARQUIN | software application, software resource | An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses. | magnetic resonance, mrs, mas, molecule, nmr spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:20878762 | Free, Available for download, Freely available | nlx_156002 | http://www.nitrc.org/projects/tarquin | SCR_002598 | TARQUIN MRS analysis package | 2026-08-04 09:40:41 | 58 | |||||
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FP-CIT SPECT brain template in MNI space Resource Report Resource Website 1+ mentions |
FP-CIT SPECT brain template in MNI space (RRID:SCR_013668) | software toolkit, software library, software resource | The FP-CIT SPECT brain template has been created using a fully automatic procedure involving posterization of the source image to three levels: background, brain and striatum. We performed a spatial affine registration of these 40 posterized source images to a posterized reference image in the MNI space. The intensity values of the transformed images is normalized linearly, assuming that the histogram of the intensity values follows an alpha-stable distribution. Lastly, we built the [123I]FP-CIT SPECT template by the mean of the transformed and normalized images. More info: 1) Salas-Gonzalez et al. Building a FP-CIT SPECT brain template using a posterization approach. Accepted in Neuroinformatics. 2) Salas-Gonzalez et al. Linear intensity normalization of FP-CIT SPECT brain images using the alpha-stable distribution. NeuroImage, Volume 65, 2013, pp. 449-455. http://dx.doi.org/10.1016/j.neuroimage.2... | SPECT, MRI, MNI |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Granada; Granada; Spain |
MICINN of Spain TEC2008-02113; MICINN of Spain TEC2012-34306; Consejeria de Innovacion Ciencia y Empresa Excellence Project P07-TIC-02566; Consejeria de Innovacion Ciencia y Empresa Excellence Project P09-TIC- 4530; Consejeria de Innovacion Ciencia y Empresa Excellence Project P11-TIC-7103 |
Attribution Non-Commercial Share Alike | SciRes_000197 | SCR_013668 | 2026-08-05 10:46:03 | 1 | ||||||||
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Laplace Beltrami Filter on QuadEdge Meshes Resource Report Resource Website |
Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) | data acquisition software, data processing software, software application, software resource | A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface. | data acquisition software, filter, laplace beltrami, surface harmonic |
is used by: Insight Segmentation and Registration Toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIBIB R01-EB008171-01A1; NCRR P41-RR015241 |
Available to the research community | SCR_014133 | Laplace-Beltrami Filter on QuadEdge Meshes | 2026-08-05 10:46:02 | 0 | ||||||||
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libSBML Resource Report Resource Website 10+ mentions |
libSBML (RRID:SCR_014134) | data or information resource, catalog, database | A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications. | markup language, systems biology, programming library, catalog | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Open source | http://sourceforge.net/p/sbml/code/HEAD/tree/ | SCR_014134 | Systems Biology Markup Language Library, Library for Systems Biology Markup Language | 2026-08-05 10:46:07 | 39 | ||||||||
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MARS (Multi-Atlas Robust Segmentation) Resource Report Resource Website 1+ mentions |
MARS (Multi-Atlas Robust Segmentation) (RRID:SCR_014137) | data processing software, segmentation software, image analysis software, software application, software resource | Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods. | segmentation software, anatomical structure, label, multi atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:24315359 | Available to the research community | SCR_014137 | 2026-08-05 10:46:07 | 5 | |||||||||
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minc-toolkit Resource Report Resource Website 1+ mentions |
minc-toolkit (RRID:SCR_014138) | data processing software, software application, software toolkit, software resource, image processing software | A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp. | image processing, software package |
uses: minc-toolkit-testsuite is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Available to the research community | http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit, https://github.com/BIC-MNI/minc-toolkit | SCR_014138 | MINC Tool Kit | 2026-08-05 10:46:05 | 6 |
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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 U24DK097771.
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