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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HERMES Resource Report Resource Website 100+ mentions |
HERMES (RRID:SCR_009584) | HERMES | data processing software, software application, software resource, software toolkit | A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis. | clinical neuroinformatics, computational neuroscience, connectivity analysis, directed transfer analysis, eeg, meg, electrocorticography, granger causality, information theory, matlab, partial directed coherence, transfer entropy analysis, connectivity, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Polytechnic University of Madrid; Madrid; Spain |
Ministry of Education of the Community of Madrid NEUROTEU-CM program S2010/BMD-2460; Spanish Ministry of Economy and Competitiveness TEC2012-38453-CO4-01; Spanish Ministry of Economy and Competitiveness TEC2012-38453-CO4-03 |
GNU General Public License | nlx_155770 | http://www.nitrc.org/projects/hermes | SCR_009584 | HERramientas de MEdida de la Sincronizacion | 2026-02-16 09:47:27 | 136 | |||||
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DTI Fiber Tract Statistics Resource Report Resource Website 1+ mentions |
DTI Fiber Tract Statistics (RRID:SCR_009460) | DTI Fiber Tract Statistics | data processing software, software application, software resource, image analysis software | This is a command line tool which allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts. Various tract-oriented scalar diffusion measures obtained from DTI brain images, are treated as a continuous function of white matter fibers'' arc-length. To analyze the trend along a given fiber tract, a command line tool performs kernel regression on this data. The idea is to try out different noise models and maximum likelihood estimates within kernel windows (along the tract), such that they best represent the data and are robust to noise and Partial Volume effect. The package contains several command line based modules and an GUI based tool called DTIAtlasFiberAnalyzer to access most functions. The features available in the tool currently, its use and input / output formats and other relevant details are provided in the first draft of the documentation. (http://www.na-mic.org/Wiki/index.php/Projects:dtistatisticsfibers). | c, linux, magnetic resonance, posix/unix-like, regression, statistical operation, dti | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | 3D Slicer License | nlx_155606 | SCR_009460 | 2026-02-16 09:47:24 | 3 | ||||||||
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INIA19 Primate Brain Atlas Resource Report Resource Website 1+ mentions |
INIA19 Primate Brain Atlas (RRID:SCR_009498) | INIA19 Primate Brain Atlas | reference atlas, data or information resource, atlas | Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas. | atlas data, magnetic resonance, nifti, neuromaps, brain atlas, mri, minimum-deformation template |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainInfo has parent organization: Integrative Neuroscience Initiative on Alcoholism |
PMID:23230398 | Creative Commons Attribution License | nlx_155646 | SCR_009498 | 2026-02-16 09:47:25 | 3 | |||||||
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Graphtools Resource Report Resource Website 1+ mentions |
Graphtools (RRID:SCR_009490) | Graphtools | data processing software, software application, software resource | A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user | magnetic resonance, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Connectivity Toolbox |
BSD License | nlx_155638 | SCR_009490 | 2026-02-16 09:47:25 | 4 | ||||||||
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resting-state pediatric imaging template Resource Report Resource Website |
resting-state pediatric imaging template (RRID:SCR_009647) | resting-state pediatric imaging template | reference atlas, data or information resource, atlas | Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates. | analyze, atlas data, magnetic resonance, child, resting-state, pediatric, adolescent | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public Domain | nlx_155978 | SCR_009647 | 2026-02-16 09:47:27 | 0 | ||||||||
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factory t1 dti Resource Report Resource Website |
factory t1 dti (RRID:SCR_009523) | factory_t1_dti | data processing software, software application, software resource, image analysis software | Tools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images. | magnetic resonance, analyze, t1, dti | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155684 | SCR_009523 | factory t1 dti | 2026-02-16 09:47:25 | 0 | ||||||||
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GRETNA Resource Report Resource Website 100+ mentions |
GRETNA (RRID:SCR_009487) | GRETNA | data processing software, software application, software resource | A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field. | computational neuroscience, eeg, meg, electrocorticography, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Functional Connectivity Analysis Tool for near-infrared spectroscopy data |
GNU General Public License | nlx_155634 | SCR_009487 | 2026-02-16 09:47:25 | 390 | ||||||||
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Generalized Covariance Analysis Resource Report Resource Website 1+ mentions |
Generalized Covariance Analysis (RRID:SCR_009488) | gCVA | data processing software, software application, software resource, image analysis software | A platform for any Principal Component Analysis (PCA)-based analysis on functional neuroimaging data (PET and fMRI). Includes: * Ordinal Trend Canonical Variance Analysis for parametric designs (C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645) * Partial Least Squares for any design matrix * Subprofile Scaling Model for cross-sectional designs (JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.) | magnetic resonance, pet, spect, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155635 | SCR_009488 | Generalized Covariance Analysis (gCVA) | 2026-02-16 09:47:25 | 8 | |||||||
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GAMMA Resource Report Resource Website 500+ mentions |
GAMMA (RRID:SCR_009484) | GAMMA | data processing software, software application, software resource, image analysis software | GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian, multivariate, nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis, lesion-deficit analysis, and functional MR data analysis. | reusable library, analyze, c, c++, console (text based), computed tomography, cygwin, hp-ux, linux, macos, microsoft, modeling, magnetic resonance, nifti, pet, spect, posix/unix-like, quantification, statistical operation, volumetric analysis, win32 (ms windows), windows, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155632 | SCR_009484 | GAMMA Suite | 2026-02-16 09:47:25 | 653 | |||||||
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AutoSeg Resource Report Resource Website 10+ mentions |
AutoSeg (RRID:SCR_009438) | AutoSeg | data processing software, software application, software resource, image analysis software | A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes. | analyze, c++, expectation minimization, image-to-image, image-to-template, labeling, linux, macos, microsoft, magnetic resonance, nonlinear warp, nrrd, posix/unix-like, region of interest, registration, resampling, segmentation, spatial transformation, spline interpolation, volumetric analysis, warping, win32 (ms windows), windows, workflow, pediatric, adolescent, adult, young |
is used by: UNC-Wisconsin Neurodevelopment Rhesus MRI Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
BSD License | nlx_155582 | SCR_009438 | 2026-02-16 09:47:24 | 23 | ||||||||
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BXH/XCEDE Tools Resource Report Resource Website 1+ mentions |
BXH/XCEDE Tools (RRID:SCR_009439) | BXH/XCEDE Tools | data processing software, software application, software resource, image analysis software | A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts. | analyze, c, c++, console (text based), dicom, format conversion, linux, macos, mgh/mgz, microsoft, minc, magnetic resonance, nifti, perl, posix/unix-like, quantification, sh/bash, statistical operation, unix shell, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Function BIRN |
BIRN License | nlx_155583 | SCR_009439 | 2026-02-16 09:47:24 | 4 | ||||||||
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DSI Studio Resource Report Resource Website 500+ mentions |
DSI Studio (RRID:SCR_009557) | DSI Studio | data processing software, software application, software resource, image analysis software | A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. | analyze, c++, console (text based), dicom, diffusion mr fiber tracking, diffusion spectrum, fiber tracking, image reconstruction, linux, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, q-ball, quantification, super tensor, tensor metric, tractography, visualization, win32 (ms windows), windows, coregistration, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
BSD License | nlx_155737 | http://www.nitrc.org/projects/dsistudio | SCR_009557 | 2026-02-16 09:47:26 | 558 | |||||||
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cmrep Resource Report Resource Website |
cmrep (RRID:SCR_009434) | cmrep | data processing software, software application, software resource, image analysis software | A set of deformable modeling algorithms for shape analysis and structure-specific normalization. Applications of cm-reps include structure-specific fMRI analysis, DTI analysis, and structural brain mor | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155535 | SCR_009434 | cm-reps, continuous medial representation | 2026-02-16 09:47:24 | 0 | ||||||||
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BrainVoyager Resource Report Resource Website 100+ mentions |
BrainVoyager (RRID:SCR_013057) | data processing software, software application, software resource, image analysis software | Commercial neuroimaging software package for multi-modal data analysis and management. It has been programmed in C++ with efficient statistical, numerical, and image processing routines. It supports parallelized basic math routines on all platforms and uses modern multi-core, multi-processor hardware for demanding computational routines. | image analysis, neuroimaging, software, multi modal data, data analysis, data management, fmri, eeg, dti, meg |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is affiliated with: Turbo-BrainVoyager is related to: BrainVoyager Brain Tutor is related to: BVQXtools is related to: NeuroElf has parent organization: Brain Innovation: Home of the BrainVoyager Product Family is parent organization of: BrainVoyager: Talairach Brain Atlas |
Commercial, License varies by geographic region | SCR_014267, nif-0000-00274 | SCR_013057 | BrainVoyager QX, Brain Voyager | 2026-02-16 09:48:16 | 180 | ||||||||
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BiofilmQuant Resource Report Resource Website |
BiofilmQuant (RRID:SCR_014088) | data processing software, software application, software resource, image analysis software | A semi-automated software tool for dental plaque biofilm quantification in quantitative light-induced fluorescence (QLF) images. | image analysis software, volumetric analysis, biofilm, dental plaque, quantification, qlf image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download, Acknowledgement requested | SCR_014088 | 2026-02-16 09:48:27 | 0 | ||||||||||
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7T Structural MRI scans ATAG Resource Report Resource Website 1+ mentions |
7T Structural MRI scans ATAG (RRID:SCR_014084) | data set, data or information resource, atlas | Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases. | 7t mri, data set, atlas, basal ganglia, structural mri scan, brain, human brain, probabilistic atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Available for download | SCR_014084 | 2026-02-16 09:48:27 | 7 | ||||||||||
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CAWorks Resource Report Resource Website 1+ mentions |
CAWorks (RRID:SCR_014185) | data processing software, software application, software resource, image analysis software | A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit. | image analysis software, computational anatomy, shape analysis, plugin, subcortex, landmark placement |
is used by: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
NIMH 1R01 MH084803; NIBIB R01 EB008171; NIA 5U01AG033655; NCRR P41 RR015241; NIBIB R01 EB000975 |
Available to the research community | http://www.cis.jhu.edu/software/caworks/ | SCR_014185 | Computational Anatomy Works | 2026-02-16 09:48:32 | 1 | |||||||
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ERP PCA Toolkit Resource Report Resource Website 1+ mentions |
ERP PCA Toolkit (RRID:SCR_013105) | ERP PCA Toolkit | data processing software, software application, software resource, software toolkit | This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip. | eeg, meg, electrocorticography, matlab, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License v2 | nlx_155753 | http://www.nitrc.org/projects/erppcatoolkit | SCR_013105 | 2026-02-16 09:48:16 | 5 | |||||||
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GSA-SNP Resource Report Resource Website 10+ mentions |
GSA-SNP (RRID:SCR_013109) | GSA-SNP | data processing software, software application, software resource | A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version. | clinical neuroinformatics, computational neuroscience, imaging genomics, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Soongsil University; Seoul; South Korea |
PMID:20501604 | GNU General Public License v2 | nlx_155765, biotools:gsa-snp | https://bio.tools/gsa-snp | SCR_013109 | 2026-02-16 09:48:25 | 18 | ||||||
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ShapePopulationViewer Resource Report Resource Website 1+ mentions |
ShapePopulationViewer (RRID:SCR_014167) | data processing software, software application, software resource, image analysis software | Software that allows users to dynamically interact with multiple surfaces simultaneously. It is very useful for visualisation and comparison of 3D surfaces by also displaying their scalars or vectors attributes stored in the points, and allowing the user to simply modify the colormap. ShapePopulationViewer is available as an extension of 3D Slicer. | 3d surface, colormap, vector, interaction |
is used by: 3D Slicer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Available to the research community | SCR_014167 | 2026-02-16 09:48:36 | 3 |
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