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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Brainnetome fMRI toolkit Resource Report Resource Website |
Brainnetome fMRI toolkit (RRID:SCR_014092) | brat | software toolkit, software resource | 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 | 2026-08-02 09:06:25 | 0 | ||||||||
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cPPI Toolbox for fMRI Resource Report Resource Website 1+ mentions |
cPPI Toolbox for fMRI (RRID:SCR_009518) | cPPI Toolbox for fMRI | software toolkit, software resource | A Matlab toolbox that allows computation of task-related functional connectivity between multiple pairs of regions. Task-related functional connectivity is computed using the correlational psychophysiological interaction (cPPI) methodology described in Fornito et al. (2012) PNAS, 109: 12788-12793. The toolbox assumes that first-level design matrices have been specified and estimated using SPM5 or later. It takes as input these design matrices as well as user-extracted regional time courses and returns a matrix of pair-wise, task-related functional connectivity for each participant. The method is scalable to large networks comprising hundreds of regions and is well-suited to graph theoretic analyses and functional connectomics. One modifiable script, cPPI_master.m, can be used to run the analysis for an entire sample of participants. | reusable library, clinical neuroinformatics, computational neuroscience, connectivity analysis, imaging genomics, matlab, magnetic resonance, task, functional connectivity, region, connectivity | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155679 | SCR_009518 | 2026-08-02 09:05:51 | 1 | ||||||||
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FSL extensions Resource Report Resource Website 1+ mentions |
FSL extensions (RRID:SCR_009472) | FSL extensions | software resource, software repository | 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 | 2026-08-02 09:05:51 | 2 | |||||||||
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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 toolkit, software resource | 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 | 2026-08-02 09:06:26 | 7 | |||||||
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BetA-Series COrrelation Resource Report Resource Website 1+ mentions |
BetA-Series COrrelation (RRID:SCR_014086) | BASCO | software toolkit, software resource | 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 | 2026-08-02 09:06:41 | 1 | |||||||
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Low Resolution Electromagnetic Tomography Resource Report Resource Website 500+ mentions |
Low Resolution Electromagnetic Tomography (RRID:SCR_007077) | LORETA | software toolkit, software resource | Software package for functional imaging of human brain. Used to compute three dimensional distribution of electric neuronal activity from non-invasive measurements of scalp electric potential differences with high time resolution in millisecond range. Non-invasive intracranial time series are used for studying functional dynamic connectivity.. Current software version includes two new, improved variants of the original method: standardized (sLORETA) and exact (eLORETA). The new methods are characterized by exact localization when tested with point sources. Due to the fact that these methods are multivariate tomographies that are solutions to the inverse EEG problem, and that they are linear in nature, they will produce a low spatial resolution image for any distribution of activity. This property is not shared by naive one-at-a-time single dipole techniques. | eeg, meg, electrocorticography, eeg modeling, forward - inverse, modeling, functional, statistical, visualization, dynamic functional connectivity, microstate segmentation, electroencephalogram, nonparametric randomization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: exact Low Resolution Electromagnetic Tomography is related to: sLORETA has parent organization: University of Zurich; Zurich; Switzerland |
Roche Research Foundation | PMID:7876038 PMID:12575492 |
Free, Non-commercial | nif-0000-00323 | http://www.nitrc.org/projects/loreta | SCR_007077 | LORETA: low resolution brain electromagnetic tomography, Low Resolution Electromag TomogrAphy | 2026-08-02 09:04:50 | 560 | ||||
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Group Information Guided ICA Resource Report Resource Website |
Group Information Guided ICA (RRID:SCR_009491) | GIG-ICA | software toolkit, software resource | 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 | 2026-08-02 09:05:36 | 0 | ||||||
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Spinal Cord Toolbox Resource Report Resource Website 1+ mentions |
Spinal Cord Toolbox (RRID:SCR_014170) | software toolkit, software resource | 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 | 2026-08-02 09:06:27 | 2 | |||||||||||
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DICCCOL predictor Resource Report Resource Website |
DICCCOL predictor (RRID:SCR_009554) | DICCCOL | software toolkit, software resource | 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 | 2026-08-02 09:05:37 | 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 toolkit, software resource | 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 | 2026-08-02 09:06:13 | 0 | ||||||
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CalaTK Resource Report Resource Website |
CalaTK (RRID:SCR_009547) | CalaTK | software toolkit, software resource | 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 | 2026-08-02 09:05:37 | 0 | ||||||
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HBM Hackathon Resource Report Resource Website 1+ mentions |
HBM Hackathon (RRID:SCR_014119) | meeting resource, training resource | A multi-day event hosted by the Organization for Human Brain Mapping which features collaborative and open neuroscience projects in data analysis and methods development. Locations change annually. | conference, human brain, meeting resource |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: brainhack.org |
Open to the neuroscience community (though a fee is required to attend) | http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3281, http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1 | SCR_014119 | OHBM Annual Meeting | 2026-08-03 09:35:36 | 6 | ||||||||
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International Imaging Genetics Conference Resource Report Resource Website |
International Imaging Genetics Conference (RRID:SCR_014125) | meeting resource, training resource | An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. This annual conference features presentations from investigators world-wide and places emphasis on facilitating in-depth discussions among the participants and presenters. | meeting resource, symposium, international, imaging genetics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
http://www.imaginggenetics.uci.edu | SCR_014125 | 2026-08-03 09:35:36 | 0 | ||||||||||
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MATLAB Tutorial on Diffusion Tensor MRI Resource Report Resource Website |
MATLAB Tutorial on Diffusion Tensor MRI (RRID:SCR_009507) | MATLAB Tutorial on Diffusion Tensor MRI | narrative resource, data or information resource, training material | An on-line tutorial on how to use MATLAB for Diffusion-Weighted MRI processing. The following subjects are covered in this tutorial: Generation of Synthetic Diffusion-Weighted MRI datasets, Diffusion Tensor (DTI) Estimation from DW-MRI, DTI Visualization as a field of ellipsoids, Higher-order Diffusion Tensor Estimation from DW-MRI, Computing of Tensor Orientation Distribution Functions (Tensor ODF), Computing of Fiber Orientations, Higher-order Diffusion Tensor Image Visualization as fields of spherical functions, Multi-fiber reconstruction etc. The tutorial contains numerous illustrations, figures and Matlab scripts embedded in the text. The reader/user can automatically generate Matlab script for a self-designed DW-MRI experiment by selecting which steps needs to be followed. The code that corresponds to the selected steps is then appropriately merged in the Matlab Script Generator, and the user can easily copy and paste the produced code directly to the Matlab command prompt. | magnetic resonance, dti, matlab, mri, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155656 | SCR_009507 | 2026-08-03 09:34:05 | 0 | |||||||||
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Maps4Mipav (Exploratory JIST) Resource Report Resource Website |
Maps4Mipav (Exploratory JIST) (RRID:SCR_000613) | Maps4Mipav, | software resource, source code | 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 | 2026-08-03 09:31:06 | 0 | |||||||
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NIRx NIRS Neuroimaging Resource Report Resource Website 10+ mentions |
NIRx NIRS Neuroimaging (RRID:SCR_002491) | material resource, instrument supplier | Commercial technology solutions for NIRS neuroscience imaging applications. | hardware, image reconstruction, nirs, fnir, optical imaging, physiological recording, tomography, neuroimaging, adult, infant, child, imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: NIRStar is parent organization of: NIRSPORT |
Restricted | nlx_155886 | http://www.nitrc.org/projects/nirx | SCR_002491 | NIRx Optical Neuroimaging | 2026-08-03 09:31:58 | 17 | |||||||
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Bisque Resource Report Resource Website 10+ mentions |
Bisque (RRID:SCR_005564) | Bisque | software resource, source code | 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 | 2026-08-03 09:32:53 | 20 | ||||
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Hitachi Optical Topography System Resource Report Resource Website |
Hitachi Optical Topography System (RRID:SCR_000865) | Hitachi Optical Topography System | material resource, instrument supplier | An instrumental supplier which provides researchers and clinicians with sophisticated All-in-One solutions in the field of neuroscience. | hardware, nirs, fnir, optical imaging, optical imaging, physiological recording, scanner, fnirs neuroimaging, ultrasound, mri, x-ray, radiography, computed tomography | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155772 | http://www.nitrc.org/projects/hitachimedical | SCR_000865 | 2026-08-03 09:31:11 | 0 | |||||||
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MultiXplore Resource Report Resource Website 1+ mentions |
MultiXplore (RRID:SCR_014814) | data processing software, software application, software resource, data analysis software | Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data. | gui, graphical user interface, cortical region, functional connectivity matrix, 3d, brain, grey matter, fiber bundle |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Western University; Ontario; Canada is a plug in for: 3D Slicer |
NSERC | Available for download | SCR_014814 | 2026-08-04 09:43:32 | 1 | |||||||||
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Automatic Tractography-based Parcellation Pipeline Resource Report Resource Website 1+ mentions |
Automatic Tractography-based Parcellation Pipeline (RRID:SCR_014815) | ATPP | data processing software, software application, software resource, workflow software | Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). " | pipeline, integrated pipeline, tractography, brain, parcel, gui, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China10.13039/501100001809 911323013162010390581501179 | Available for download | https://doi.org/10.5281/zenodo.239705, https://doi.org/10.5281/zenodo.239702 | https://github.com/haililihai/ATPP_CLI, https://github.com/haililihai/ATPP_GUI | SCR_014815 | Automatic Tractography-based Parcellation Pipeline (ATPP) | 2026-08-04 09:43:31 | 2 |
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