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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FSL extensions Resource Report Resource Website 1+ mentions |
FSL extensions (RRID:SCR_009472) | FSL extensions | software repository, software resource | A reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL |
nlx_155619 | SCR_009472 | 2026-09-19 12:58:06 | 2 | |||||||||
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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 | 2026-09-19 12:58:07 | 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 | 2026-09-19 12:58:07 | 18 | |||||
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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 | 2026-09-19 12:58:07 | 3 | |||||
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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 | 2026-09-19 12:58:07 | 242 | ||||||
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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 | 2026-09-19 12:58:07 | 0 | ||||||||
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Group Information Guided ICA Resource Report Resource Website |
Group Information Guided ICA (RRID:SCR_009491) | GIG-ICA | software resource, software toolkit | Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too. | computational neuroscience, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
Hundred Talent Program of the Chinese Academy of Sciences ; National Basic Research Program of China 973 Program ; National Natural Science Foundation of China 91132707; National Natural Science Foundation of China 30970770 |
PMID:23194820 | Available for download | nlx_155639 | SCR_009491 | 2026-09-19 12:58:07 | 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 | 2026-09-19 12:58:07 | 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 | 2026-09-19 12:58:07 | 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 | 2026-09-19 12:58:07 | 58 | ||||||||
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DICCCOL predictor Resource Report Resource Website |
DICCCOL predictor (RRID:SCR_009554) | DICCCOL | software resource, software toolkit | A software toolbox to predict 358 DICCCOL landmarks (Dense Individualized and Common Connectivity-based Cortical landmarks (http://dicccol.cs.uga.edu) ) on a new brain given b0, brain surface data and DTI derived fiber data (vtk format). Each DICCCOL landmark is defined by group-wise consistent white-matter fiber connection patterns derived from diffusion tensor imaging (DTI) data. DICCCOL aims to provide large-scale cortical landmarks with finer granularity, better functional homogeneity, more accurate functional localization, and automatically-established cross-subjects correspondence. | c++, linux, magnetic resonance, posix/unix-like, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Georgia; Georgia; USA |
Open unspecified license, GPL-Style Open unspecified license | nlx_155734 | http://www.nitrc.org/projects/dicccol_0_1 | SCR_009554 | Dense Individualized and Common Connectivity-based Cortical Landmarks predictor | 2026-09-19 12:58:07 | 0 | ||||||
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CalaTK Resource Report Resource Website |
CalaTK (RRID:SCR_009547) | CalaTK | software resource, software toolkit | An open-source toolkit for cross-sectional and longitudinal atlas building. The CalaTK project develops innovative methods and tools for longitudinal atlases with a focus on neurodevelopment. The computational toolbox is developed with the objective to analyze the neural developmental patterns observed in human and non-human primate structural and diffusion tensor magnetic resonance (MR) images. | reusable library, atlas application, c++, computational neuroscience, image-to-image, magnetic resonance, registration, software, spatial transformation, structural mri, diffusion tensor image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Fluid Registration and Atlas Toolkit |
Apache License v2 | nlx_155727 | http://www.nitrc.org/projects/calatk | SCR_009547 | CalaTK - Atlas Building TK | 2026-09-19 12:58:07 | 0 | ||||||
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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 | 2026-09-19 12:58:07 | 6 | |||||
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Brainnetome fMRI toolkit Resource Report Resource Website |
Brainnetome fMRI toolkit (RRID:SCR_014092) | brat | software resource, software toolkit | An fMRI toolkit which contains a large selection of complex network measures in Matlab GUI. These measures are increasingly used to characterize structural and functional brain connectivity datasets. | software toolkit, fmri, human brain, brain structure, brain connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Brainnetome Atlas Viewer has parent organization: Chinese Academy of Sciences; Beijing; China |
Available for download, The community can contribute to this resource | http://www.brainnetome.org/en/brat | SCR_014092 | 2026-09-19 12:58:11 | 0 | ||||||||
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GLMdenoise: a fast, automated technique for denoising task-based fMRI data Resource Report Resource Website 1+ mentions |
GLMdenoise: a fast, automated technique for denoising task-based fMRI data (RRID:SCR_014116) | software resource, software toolkit | A MATLAB toolbox for denoising task-based fMRI data. It derives noise regressors from voxels unrelated to the experimental paradigm and uses these regressors in a general linear model (GLM) analysis of the data. The technique only requires a design matrix indicating the experimental design and an fMRI dataset. | matlab toolbox, software toolkit, denoise, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Washington University in St. Louis; Missouri; USA |
McDonnell Center for Systems Neuroscience and Arts and Sciences at Washington University ; NEI F32-EY022294; NEI K99-EY022116; NEI RO1-EY03164 |
Acknowledgement Requested | http://kendrickkay.net/GLMdenoise/ | SCR_014116 | GLMdenoise | 2026-09-19 12:58:11 | 8 | |||||||
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BetA-Series COrrelation Resource Report Resource Website 1+ mentions |
BetA-Series COrrelation (RRID:SCR_014086) | BASCO | software resource, software toolkit | A software tool (with GUI) for investigating inter-regional functional connectivity in event-related fMRI data and allows the user to assess the modulation of functional connectivity by an experimental condition. | software toolkit, toolbox, functional connectivity, matlab, connectivity analysis |
uses: MarsBaR region of interest toolbox for SPM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
DOI:10.3389/fnsys.2015.00126 | Available for download | SCR_014086 | Beta-Series Correlation, Beta Series Correlation | 2026-09-19 12:58:11 | 1 | |||||||
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Spinal Cord Toolbox Resource Report Resource Website 1+ mentions |
Spinal Cord Toolbox (RRID:SCR_014170) | software resource, software toolkit | A comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. The toolbox includes a template and several atlases, along with state-of-the-art methods to register any data to the template. It also includes useful scripts for data preprocessing: extraction of centerline, automatic segmentation, slice-wise motion correction, etc. |
uses: FSL is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada has parent organization: University of Montreal; Quebec; Canada has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
http://sourceforge.net/projects/spinalcordtoolbox/ | SCR_014170 | 2026-09-19 12:58:11 | 2 | |||||||||||
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DICOMConvert Resource Report Resource Website |
DICOMConvert (RRID:SCR_014100) | software application, software resource, standalone software | 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 | 2026-09-19 12:58:11 | 0 | ||||||||
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Notion ResearchPACS Resource Report Resource Website |
Notion ResearchPACS (RRID:SCR_014154) | software application, software resource, standalone software | 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 | 2026-09-19 12:58:11 | 0 | ||||||||||
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CUDA-SPHERE-FWD-MEEG Resource Report Resource Website |
CUDA-SPHERE-FWD-MEEG (RRID:SCR_013225) | CUDA-SPHERE-FWD-MEEG | software resource, software toolkit | A CUDA C based toolkit which provides a GPU based implementation of the spherical model forward solution for the 306 channel Elekta Neuromag MEG system and the EEG. The 1-Sphere forward solution for the MEG and the 4-Sphere forward solution for the EEG is implemented in CUDA C and an accelerated solution is obtained using the NVIDIA GPU when the solution is calculated for a large number of dipoles (on the order of 15000 and above) and sensor location. Speedup by a factor of 22 and 32 is obtained for the EEG and MEG solution respectively when compared to the fastest CPU implementation available in the public domain. The complete source code and pre-compiled binaries are also made available via an open source license (GPL Version 3). A CUDA enabled NVIDIA graphics card is required to use the software. | eeg, meg, electrocorticography, eeg modeling, forward - inverse, meg modeling, modeling | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License v3 | nlx_155725 | http://www.nitrc.org/projects/cuda_sphere_fwd | SCR_013225 | CUDA accelerated spherical model M/EEG, CUDA accelerated spherical model forward solution for EEG/MEG | 2026-09-19 12:58:09 | 0 |
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