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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NKI/Rockland Sample Resource Report Resource Website 10+ mentions |
NKI/Rockland Sample (RRID:SCR_009435) | data set, data or information resource | A phenotypically rich neuroimaging sample, consisting of data obtained from individuals between the ages of 4 and 85 years-old. All individuals included in the sample undergo semi-structured diagnostic psychiatric interviews, and complete a battery of psychiatric, cognitive and behavioral assessments in order to provide comprehensive phenotypic information for the purpose of exploring brain / behavior relationships. | image collection, young human, late adult human, neuroimaging, phenotype, fmri, dti, mprage, t2, psychiatric assessment, cognitive assessment, behavioral assessment, resting state fmri, dicom, nifti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Rockland Download Link Script is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: NKI-RS Enhanced Sample has parent organization: 1000 Functional Connectomes Project |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; NKI Center for Advanced Brain Imaging CABI ; the Brain Research Foundation Chicago ; the Stavros Niarchos Foundation ; NIMH P50 MH086385-S1 |
Creative Commons Attribution-NonCommercial License | nlx_155538 | http://www.nitrc.org/projects/dl_dataset | SCR_009435 | Nathan Kline Institute / Rockland Sample, NKI Rockland Sample, Nathan Kline Institute (NKI) / Rockland Sample | 2026-08-04 09:42:22 | 17 | |||||
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CANDI Neuroimaging Access Point Resource Report Resource Website |
CANDI Neuroimaging Access Point (RRID:SCR_009542) | CANDI Neuroimaging Access Point | data set, data or information resource | A series of structural brain images, as well as their anatomic segmentations, demographic and behavioral data and a set of related morphometric resources (static and dynamic atlases) made avaialble from the Child and Adolescent NeuroDevelopment Initiative (CANDI) at UMass Medical School. Schiz Bull 2008 data is now available on NITRC-IR. Please register for access: http://www.nitrc.org/project/request.php?group_id=377 | atlas data, magnetic resonance, nifti, quantification, segmentation, software, volumetric analysis, web environment, web resource, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Massachusetts Medical School; Massachusetts; USA is parent organization of: CANDI Share: Schizophrenia Bulletin 2008 |
Creative Commons Attribution License | nlx_155721 | http://www.nitrc.org/projects/candi_share | SCR_009542 | 2026-08-04 09:42:24 | 0 | |||||||
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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 | 2026-08-04 09:42:23 | 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 | 2026-08-04 09:42:24 | 16 | ||||||
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CAMINO-TRACKVIS Resource Report Resource Website |
CAMINO-TRACKVIS (RRID:SCR_009450) | CAMINO-TRACKVIS | systems interoperability software, software application, software resource | Software package that allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital. With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts. | magnetic resonance, tractography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Camino is related to: TrackVis |
MIT License, X Consortium License | nlx_155594 | SCR_009450 | 2026-08-04 09:42:22 | 0 | ||||||||
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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 | 2026-08-04 09:42:24 | 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 | 2026-08-04 09:42:25 | 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 | 2026-08-04 09:42:24 | 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 | 2026-08-04 09:42:24 | 0 | |||||
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fMRI Artefact rejection and Sleep Scoring Toolbox Resource Report Resource Website 10+ mentions |
fMRI Artefact rejection and Sleep Scoring Toolbox (RRID:SCR_009620) | FASST | software application, software resource, software toolkit | An EEG toolbox developed to help users with 3 specific types of data and problems: simulatenous EEG-fMRI recording, continuous EEG scoring (e.g. sleep) and handling (visualisation, cutting, power spectrum, etc.) multi-channel recording of spontaneous EEG. The toolbox is written in Matlab and is specifically compatible with the BrainAmp family of EEG recorders (from BrainProducts GmbH) Three other data formats are now also supported: the edf "European Data Format", exported raw-EGI data (from Electrical Geodesics, Inc.) and the BCI2000 format.The results are directly compatible with SPM8 and are saved with SPM8 EEG data format. | eeg, meg, electrocorticography, matlab, magnetic resonance, os independent, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Liege; Wallonia; Belgium |
PMID:21461381 | GNU General Public License | nlx_155846 | http://www.nitrc.org/projects/fasst | SCR_009620 | FASST - fMRI Artefact rejection and Sleep Scoring Toolbox | 2026-08-04 09:42:25 | 17 | |||||
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BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software application, software resource | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-08-04 09:42:23 | 3 | |||||
|
BESA Resource Report Resource Website 100+ mentions |
BESA (RRID:SCR_009530) | BESA | software application, software resource | Software for source analysis and dipole localization in EEG and MEG research. BESA Research has been developed on the basis of 20 years experience in human brain research by Michael Scherg, University of Heidelberg, and Patrick Berg, University of Konstanz. BESA Research is a highly versatile and user-friendly Windows program with optimized tools and scripts to preprocess raw or averaged data for source analysis. All important aspects of source analysis are displayed in one window for immediate selection of a wide range of tools. BESA Research provides a variety of source analysis algorithms, a standardized realistic head model (FEM), and allows for fast and easy hypothesis testing and integration with MRI and fMRI. | application, connectivity analysis, eeg, meg, electrocorticography, eeg modeling, event related potential, finite element analysis, forward - inverse, fourier time-domain analysis, independent component analysis, meg modeling, modeling, principal component analysis, source separation analysis, spectral analysis, statistical operation, surrogate data analysis, temporal transformation, time domain analysis, evoked potential, evoked field, event-related field, neuroimaging, mri, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155695 | http://www.nitrc.org/projects/besa | SCR_009530 | Brain Electrical Source Analysis | 2026-08-04 09:42:25 | 233 | ||||||
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Hitachi2nirs Resource Report Resource Website |
Hitachi2nirs (RRID:SCR_009494) | Hitachi2nirs | software application, software resource | A Matlab script to convert the raw .csv Hitachi ETG4000 output file into a .nirs file for use with Homer2. The script also requires a .pos file. This is the output of the polhemus 3D digitiser that they use to record where the optodes are located spatially. I realize that not everyone uses a 3D digitiser so I have included three example .pos files - one for each of the possible optode arrangements of the Hitachi system (either two 3x3 arrays, one 3x5 array or one 4x4 array). If you use a different arrangement or have more probes than them, feel free to get in touch and they may be able to advise on how to create a model .pos file. There are two versions of the conversion script: 1. single - this will read in ONE .csv file and ONE .pos file and create ONE .nirs file 2. multi - this will read in a user-specified number of .csv files and ONE .pos file. It will then create one .nirs file for each .csv file that was read in and deposit it in the same directory as that .csv file. | hardware, matlab, nirs, fnir, optical imaging, optical imaging, physiological recording | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155642 | SCR_009494 | 2026-08-04 09:42:24 | 0 | ||||||||
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ALVIN Resource Report Resource Website 1+ mentions |
ALVIN (RRID:SCR_009527) | ALVIN | software application, software resource | A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject. | magnetic resonance, quantification, region of interest, segmentation, software, volume measurement, volumetric analysis, volumetric analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155690 | http://www.nitrc.org/projects/alvin_lv | SCR_009527 | ALVIN - Automatic Lateral Ventricle delIneatioN, Automatic Lateral Ventricle delIneatioN, ALVIN - Lateral Ventricle Segmentation | 2026-08-04 09:42:24 | 6 | ||||||
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fMRI-CPCA Resource Report Resource Website 1+ mentions |
fMRI-CPCA (RRID:SCR_009520) | fMRI-CPCA, fMRI CPCA | software application, software resource | Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated. | analyze, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, principal component analysis, regression, statistical operation, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155682 | SCR_009520 | fMRI-Constrained Principal Component Analysis, fMRI Constrained Principal Component Analysis | 2026-08-04 09:42:24 | 7 | |||||||
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GAMBIT Resource Report Resource Website 50+ mentions |
GAMBIT (RRID:SCR_009483) | GAMBIT | software application, software resource | An end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module, or directly as a command line. | analyze, c++, linux, mesh generation, modeling, magnetic resonance, nrrd, posix/unix-like, surface analysis, thickness, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
BSD License | nlx_155631 | SCR_009483 | 2026-08-04 09:42:24 | 57 | ||||||||
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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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