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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Clinical Toolbox for SPM Resource Report Resource Website 1+ mentions |
Clinical Toolbox for SPM (RRID:SCR_014096) | software application, software resource, software toolbox, data management software | A clinical toolbox useful for normalizing data from individuals with brain injury and/or modalities popular in the clinical environment (CT). It supports either enantiomorphic or lesion-masked normalization. It can be either scripted or used with SPM's simple graphical interface. | software toolkit, clinical toolbox, normalization, data management software, human brain, brain injury, spm |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: SPM has parent organization: University of South Carolina; South Carolina; USA |
Available for download | http://www.mccauslandcenter.sc.edu/CRNL/clinical-toolbox | SCR_014096 | 2026-08-04 09:43:20 | 9 | |||||||||
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Neoseg Resource Report Resource Website 1+ mentions |
Neoseg (RRID:SCR_014144) | segmentation software, data processing software, software resource, software application, image analysis software | A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior. | segmentation software, automatic segmentation, neonatal brain mri |
is used by: NeoSegPipeline is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Available to the research community | https://github.com/NIRALUser/neoseg/tree/master | SCR_014144 | 2026-08-04 09:43:21 | 2 | |||||||||
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NeoSegPipeline Resource Report Resource Website |
NeoSegPipeline (RRID:SCR_014145) | segmentation software, data processing software, software resource, software application, image analysis software | This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results. | segmentation software, atlas, brain mri, diffusion image |
uses: Neoseg uses: NIRAL Utilities is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: UNC Human Brain Atlas |
Available to the research community | https://github.com/marie-cherel2013/NeosegPipeline/tree/master/NeosegPipeline | SCR_014145 | 2026-08-04 09:43:20 | 0 | |||||||||
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Neuron-C Resource Report Resource Website 1+ mentions |
Neuron-C (RRID:SCR_014148) | simulation software, software application, software resource, source code | A simulation language for modeling biophysically realistic neural circuits (1 to 10,000 neurons) and simulating physiology experiments on it. Programs for plotting and displaying data are included. | simulation, simulation language, source code, neural circuit |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
Available to the research community | http://retina.anatomy.upenn.edu/~rob/neuronc.html | SCR_014148 | NeuronC Neural Simulation Language, Neuron C Neural Simulation Language, NeuronC | 2026-08-04 09:43:21 | 7 | ||||||||
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NIH Pediatric MRI Data Repository Resource Report Resource Website |
NIH Pediatric MRI Data Repository (RRID:SCR_014149) | NIHPD | database, data or information resource, image collection | A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult. | database, image collection, structural mri, dti, spectroscopy, human brain, child |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
NICHD ; National Institute on Drug Abuse ; NIMH ; NINDS |
Available to the research community, Access must be granted | http://pediatricmri.nih.gov/nihpd/info/index.html | SCR_014149 | Pediatric MRI Data Repository, NIH MRI Study of Normal Brain Development Pediatric MRI Data Repository | 2026-08-04 09:43:21 | 0 | ||||||
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MISST - Microstructure Imaging Sequence Simulation ToolBox Resource Report Resource Website 1+ mentions |
MISST - Microstructure Imaging Sequence Simulation ToolBox (RRID:SCR_014140) | MISST | simulation software, software application, software resource, software toolkit | A practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. It is designed for diffusion MRI researchers who are interested in understanding and developing diffusion pulse sequences for imaging microstructure. | simulation software, software toolkit, mri simulator, pulse sequence, tissue model, imaging, microstructure |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Available to the research community | http://mig.cs.ucl.ac.uk/index.php?n=Tutorial.MISST | SCR_014140 | Microstructure Imaging Sequence Simulation Toolbox | 2026-08-04 09:43:21 | 2 | |||||||
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Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation Resource Report Resource Website |
Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation (RRID:SCR_014108) | data processing software, data visualization software, software application, software resource | A tool which offers a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units (GPUs). The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data. | data visualization software, myelin map, t2 data, parallel computation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of British Columbia; British Columbia; Canada |
MS/MRI Research Group at the University of British Columbia ; Natural Sciences and Engineering Research Council of Canada ; Milan and Maureen Ilich Foundation |
Available for download | SCR_014108 | 2026-08-04 09:43:20 | 0 | |||||||||
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Forward: Accurate finite element electromagnetic head models Resource Report Resource Website 1+ mentions |
Forward: Accurate finite element electromagnetic head models (RRID:SCR_014109) | simulation software, software application, software resource | A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included. | model, simulation software, electromagnetic head model, eeg forward modeling, mapping |
uses: Nipype is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Liege; Wallonia; Belgium |
Belgian National Fund for Scientific Research ; Marie Curie Initial Training Network in Neurophysics PITN-GA-2009-238593 |
SCR_014109 | Forward | 2026-08-04 09:43:20 | 8 | |||||||||
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ERPwavelab Resource Report Resource Website 1+ mentions |
ERPwavelab (RRID:SCR_014106) | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain. | software toolbox, data analysis, data visualization, eeg data, meg data, plugin, time frequency domain, fourier time domain analysis, temporal wavelet analysis |
is used by: EEGLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Technical University of Denmark; Lyngby; Denmark |
Open source | http://www.erpwavelab.org | SCR_014106 | 2026-08-04 09:43:20 | 9 | |||||||||
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Functional Connectivity Analysis Tool for near-infrared spectroscopy data Resource Report Resource Website 1+ mentions |
Functional Connectivity Analysis Tool for near-infrared spectroscopy data (RRID:SCR_014111) | FC-NIRS | data processing software, data analysis software, software resource, software application, network analysis software | A functional connectivity analysis tool for near-infrared spectroscopy data. Its functions include preprocessing, quality control, FC calculation and network analysis. | network analysis, data processing software, functional connectivity analysis, near infrared spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: GRETNA has parent organization: Beijing Normal University; Beijing; China |
Natural Science Foundation of China 81201122; Natural Science Foundation of China 81571755; Fundamental Research Funds for the Central Universities 2012LYB06; Beijing Natural Science Foundation Z111107067311036; Specialized Research Fund for the Doctoral Program of Higher Education ; Open Research Fund of the State Key Laboratory of Cognitive Neuroscience and Learning |
Available for download | SCR_014111 | 2026-08-04 09:43:20 | 1 | ||||||||
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GazeReader Resource Report Resource Website 1+ mentions |
GazeReader (RRID:SCR_014112) | data processing software, software resource, software application, software toolkit, data acquisition software | A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment. | software toolkit, data acquisition software, eye tracking, glm analysis, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Iowa; Iowa; USA |
Free for non-commercial use only | http://www.nitrc.org/projects/gazereader | SCR_014112 | 2026-08-04 09:43:20 | 1 | |||||||||
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freesurfR Resource Report Resource Website |
freesurfR (RRID:SCR_014110) | data processing software, data analysis software, software resource, software application, software toolkit | A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2. | data analysis software, software package, group analysis, freesurfer, surface data, r linear model |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Available for download | SCR_014110 | 2026-08-04 09:43:20 | 0 | ||||||||||
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gCCA Resource Report Resource Website 10+ mentions |
gCCA (RRID:SCR_014113) | data processing software, software application, software resource, data analysis software | A multivariate method for fMRI data analysis based on generalized canonical correlation analysis (gCCA) to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. For multiple subjects, gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects. | data analysis software, multivariate method, fmri data analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Toronto; Ontario; Canada |
University of Tehran 8101079/01/01; CIHR MOP 84483; Heart and Stroke Foundation of Ontario |
Available for download | SCR_014113 | 2026-08-04 09:43:20 | 16 | |||||||||
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Graph Theory GLM (GTG) MATLAB Toolbox Resource Report Resource Website 1+ mentions |
Graph Theory GLM (GTG) MATLAB Toolbox (RRID:SCR_014075) | GTG | data processing software, software application, software resource, data analysis software | A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times. | MATLAB, Connectivity Analysis, fMRI, data analysis software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Boston University; Massachusetts; USA |
http://sites.bu.edu/metalab/tools/ | SCR_014075 | Graph Theory GLM, GTG MATLAB Toolbox | 2026-08-04 09:43:19 | 5 | ||||||||
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GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity Resource Report Resource Website 10+ mentions |
GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity (RRID:SCR_014117) | data processing software, data analysis software, software resource, software application, software toolkit | A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results. | software toolbox, data analysis, brain connectivity, graph theoretical analysis, statistical analysis, network construction, network characterization |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:25725332 | Available for download | http://www.rfmri.org/GraphVar | SCR_014117 | GraphVar | 2026-08-04 09:43:20 | 33 | |||||||
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HAMMER: Deformable Registration Resource Report Resource Website |
HAMMER: Deformable Registration (RRID:SCR_014118) | data processing software, software application, image processing software, software resource | A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. | image processing, software package, warp, brain image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_014118 | 2026-08-04 09:43:20 | 0 | ||||||||||
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MGA - Multimodal Glioma Analysis Resource Report Resource Website 1+ mentions |
MGA - Multimodal Glioma Analysis (RRID:SCR_014122) | MGA | data processing software, standalone software, software resource, software application, workflow software, image analysis software | An MRI preprocessing pipeline built with HOF (Heterogeneous Optimization Framework) methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis in both longitudinal and cross-sectional studies. It works on DICOM images from a single MRI study and includes perfusion (DSC sequence based) analysis and DTI analysis. MGA spatially co-registers all study images to an atlas template and to a template image within the study. | image analysis, workflow software, standalone, pipeline, mri, heterogeneous optimization framework, clinical image study, image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014122 | Multimodal Glioma Analysis | 2026-08-04 09:43:20 | 1 | ||||||||
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bic-mni-models Resource Report Resource Website 10+ mentions |
bic-mni-models (RRID:SCR_014087) | data or information resource, image collection | Anatomical brain template library which includes models from ICBM 2009 template.Number of unbiased non-linear averages of MNI152 database have been generated that combines attractions of both high-spatial resolution and signal-to-noise while not being subject to vagaries of any single brain. Procedure involved multiple iterations of process where, at each iteration, individual native MRIs were non-linearly fitted to the average template from previous iteration, beginning with MNI152 linear template. | brain template, anatomical brain library, image collection, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ICBM 152 Nonlinear atlases version 2009 has parent organization: McGill University; Montreal; Canada |
SCR_014087 | 2026-08-04 09:43:19 | 44 | |||||||||||
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Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 Resource Report Resource Website |
Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 (RRID:SCR_014127) | data processing software, software resource, software application, 3d visualization software, data visualization software | A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers. | filter, data visualization software, 3d visualization, tractography, algorithm, fiber tracking, HARDI |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NINDS NS066340 | Available for download | http://www.cise.ufl.edu/~salehian/Softwares.html | SCR_014127 | IUKF Tractography Software v1.0, IUKF Tractography Software, Intrinsic Unscented Kalman Filter Tractography Software, Intrinsic Unscented Kalman Filter Tractography Software v1.0 | 2026-08-04 09:43:20 | 0 | |||||||
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Turbo-BrainVoyager Resource Report Resource Website 1+ mentions |
Turbo-BrainVoyager (RRID:SCR_014175) | data processing software, standalone software, software resource, software application, image analysis software, data visualization software | A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal). | image analysis software, data visualization software, standalone software, neurofeedback, mri analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: BrainVoyager has parent organization: Brain Innovation: Home of the BrainVoyager Product Family |
Public, Commercial | http://www.brainvoyager.com/TurboBrainVoyager.html | SCR_014175 | 2026-08-04 09:43:21 | 2 |
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