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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Brain Catalogue Resource Report Resource Website |
Brain Catalogue (RRID:SCR_009442) | Brain Catalogue | data or information resource, source code, software resource | High quality data, open and freely available to everyone to celebrate the diversity of the vertebrate brain. Do you have data that you would like to share? Do not hesitate to contact them! The Brain Catalogue is developed by Florencia Grisanti (Taxidermy Workshop of the Natural History Museum in Paris) and Roberto Toro (Neuroscience Department of the Institut Pasteur). Many of our specimens come from the Vertebrate Brain Collection of the Jardin des Plantes, curated by Marc Herbin, and are scanned at the Institut du Cerveau et de la Moelle (ICM) by Mathieu Santin and Alexandra Petiet, from the CENIR laboratory, with financial and methodological support kindly provided by Olivier Colliot, head of the Cogimage team at the ICM. | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Other/Commercial license License | nlx_155586 | SCR_009442 | The Brain Catalogue | 2026-02-15 09:20:12 | 0 | ||||||||
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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 | 2026-02-15 09:18:03 | 0 | |||||
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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 | 2026-02-15 09:18:20 | 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 | 2026-02-15 09:18:20 | 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 | 2026-02-15 09:18:20 | 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 | 2026-02-15 09:18:20 | 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 | 2026-02-15 09:18:20 | 12132 | |||||
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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 | 2026-02-15 09:18:19 | 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 | 2026-02-15 09:18:21 | 58 | |||||
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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 | 2026-02-15 09:19:18 | 1975 | |||||
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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 | 2026-02-15 09:17:58 | 0 | |||||||
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RT Image Resource Report Resource Website 10+ mentions |
RT Image (RRID:SCR_002535) | RT_Image | software application, software resource | Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data. | computed tomography, magnetic resonance, optical imaging, pet, spect, mri, dicom |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford University School of Medicine; California; USA |
PMID:17375973 | Free, Available for download, Freely available | nlx_155940 | http://www.nitrc.org/projects/rt_image | SCR_002535 | 2026-02-15 09:18:19 | 10 | ||||||
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Maps4Mipav (Exploratory JIST) Resource Report Resource Website |
Maps4Mipav (Exploratory JIST) (RRID:SCR_000613) | Maps4Mipav, | source code, software resource | The exploratory development tree of Java Image Science Toolkit (JIST), an extension to the MIPAV (Medical Image Processing, Analysis, and Visualization) plug-in framework that allows the user to design and execute pipelines, which are multi-stage processing tasks.. New features and designs are tested here before general release into the JIST project. JIST was formerly known as the MedIC Automated Pipeline Scheduler (MAPS). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit is related to: MIPAV: Medical Image Processing and Visualization |
Free, Available for download, Freely available | nlx_151345 | SCR_000613 | MedIC Automated Pipeline Scheduler Medical Image Processing Analysis and Visualization | 2026-02-15 09:17:57 | 0 | |||||||
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Bisque Resource Report Resource Website 10+ mentions |
Bisque (RRID:SCR_005564) | Bisque | source code, software resource | A scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content. New features and testing of Bisque version: 0.5.1, among many others are: # Parallel execution of datasets # Rich interfaces for autogenerated module UI # Abstracted storage system for local, irods, etc.. They are using Mercurial for their source control system. This should be installed before proceeding. Browse source on-line, http://biodev.ece.ucsb.edu/projects/bisquik/browser Bisque Installation, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/InstallationInstructions05 Bisque DOWNLOAD, http://biodev.ece.ucsb.edu/projects/bisquik/wiki/download, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | image, biology, annotate, metadata, analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Center for Bio-Image Informatics |
NSF ITR-0331697; NSF IIS-0808772 |
PMID:20031971 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144653 | http://www.nitrc.org/projects/bisque | SCR_005564 | Bio-Image Semantic Query User Environment, Bisque - Bio-Image Semantic Query User Environment | 2026-02-15 09:19:00 | 20 | ||||
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DICOM UploadGUI Resource Report Resource Website |
DICOM UploadGUI (RRID:SCR_009458) | DICOM_UploadGUI | software application, software resource | A Java tool that takes an unorganized collection of DICOM scans, sorts and categorizes them according to user-customizable rules, gathers metadata about the scans, and saves out this information to help facilitate data uploads. Batch pr | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155604 | SCR_009458 | DICOM UploadGUI | 2026-02-15 09:19:44 | 0 | ||||||||
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FMRIpower Resource Report Resource Website 10+ mentions |
FMRIpower (RRID:SCR_009576) | fmripower | software application, software resource | An easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data. | analyze, linear, matlab, magnetic resonance, nifti, regression, statistical operation, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA |
PMID:17919925 | Public Domain | nlx_155757 | http://www.nitrc.org/projects/fmripower | SCR_009576 | 2026-02-15 09:19:46 | 16 | ||||||
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EEProbe Resource Report Resource Website 10+ mentions |
EEProbe (RRID:SCR_009570) | eeprobe | software application, software resource | A complete software package for the study of event-related brain activity with high-resolution EEG/MEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig, Germany, and is available for other institutions through ANT Neuro B.V., The Netherlands, enhanced with the EEProbe Databrowser. ERP investigations, both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities. All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively, external data can be imported from a multitude of formats. Processing in EEProbe makes use of open file formats (see LIBEEP) and is designed to integrate with ASA for advanced source analysis. EEProbe is available for Linux and Mac OS X. | eeg, meg, electrocorticography, event related potential, time domain analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155750 | http://www.nitrc.org/projects/eeprobe | SCR_009570 | 2026-02-15 09:20:09 | 26 | |||||||
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E-Prime Extensions for fMRI Resource Report Resource Website |
E-Prime Extensions for fMRI (RRID:SCR_009568) | EEfMRI | software application, software resource | Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime. | experimental control, microsoft, magnetic resonance, win32 (ms windows), windows, windows vista, windows xp, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Other/Commercial license License | nlx_155748 | http://www.nitrc.org/projects/eefmri | SCR_009568 | 2026-02-15 09:19:45 | 0 | |||||||
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Finsler tractography module for Slicer Resource Report Resource Website |
Finsler tractography module for Slicer (RRID:SCR_009477) | Finsler tractography module for Slicer | software application, software resource | This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost. The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles (VTK required). The software can be built as either a stand-alone or a CLI plugin for 3D Slicer. | c++, connectivity analysis, console (text based), diffusion mr fiber tracking, diffusion spectrum, direction, fiber tracking, linux, macos, microsoft, modeling, magnetic resonance, nrrd, posix/unix-like, q-ball, super tensor, tensor metric, tractography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is parent organization of: Fiber-tracking based on Finsler distance |
3D Slicer License | nlx_155624 | SCR_009477 | 2026-02-15 09:20:08 | 0 | ||||||||
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LONI De-identification Debablet Resource Report Resource Website |
LONI De-identification Debablet (RRID:SCR_009593) | LONI De-identification Debablet | software application, software resource | Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner. | analyze, console (text based), dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155784 | http://www.nitrc.org/projects/did | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23 | SCR_009593 | 2026-02-15 09:20:05 | 0 |
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