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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Group ICA of fMRI Toolbox Resource Report Resource Website 1000+ mentions |
Group ICA of fMRI Toolbox (RRID:SCR_001953) | GIFT | data processing software, software resource, software application, image analysis software, software toolkit | Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki. | independent component analysis, matlab, magnetic resonance, fmri, algorithm |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Group ICA Of EEG Toolbox has parent organization: MIALAB - Medical Image Analysis Lab |
NIBIB 1R01EB000840 | PMID:18165105 | Free, Available for download, Freely available | SCR_024416, nif-0000-00309 | http://www.nitrc.org/projects/gift | http://mialab.mrn.org/software/gift/ | SCR_001953 | Group ICA Of fMRI Toolbox (GIFT) | 2026-08-04 09:40:31 | 1411 | |||
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OBART Resource Report Resource Website 1+ mentions |
OBART (RRID:SCR_001903) | OBART | web application, software resource, atlas, data or information resource | Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases. | atlas, brain, clinical, mapping, meta-analysis, neuroscience, visualization, label |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Architecture Project has parent organization: Boston University; Massachusetts; USA |
NIMH 5R01MH084802 | PMID:19787067 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10473 | http://www.nitrc.org/projects/obart | http://obart.brainarchitecture.org | SCR_001903 | The Online Brain Atlas Reconciliation Tool, Online Brain Atlas Reconciliation Tool | 2026-08-04 09:40:30 | 2 | |||
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NeuroMorpho.Org Resource Report Resource Website 50+ mentions |
NeuroMorpho.Org (RRID:SCR_002145) | storage service resource, data repository, service resource, database, data or information resource | Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact. | neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurology, FASEB list |
is used by: NIF Data Federation is used by: BICCN is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: DONE: Detection of Outlier NEurons is related to: NIF Literature is related to: Computational Neurobiology and Imaging Center is related to: Integrated Manually Extracted Annotation is related to: xyz2swc is related to: Allen Institute for Brain Science has parent organization: George Mason University; Virginia; USA is parent organization of: NeuroMorpho.Org species ontology is parent organization of: NeuroMorpho.Org species ontology old |
NINDS R01 NS39600; MURI ONR N000141010198 |
PMID:17728438 PMID:16552417 PMID:18949582 |
Free, Available for download, Freely available | nif-0000-00006, r3d100010107 | http://www.nitrc.org/projects/neuromorpho_org, http://neuromorpho.org/, https://doi.org/10.17616/R3WW2K | SCR_002145 | Neuro Morpho, NeuroMorpho.org, NeuroMorpho | 2026-08-04 09:40:34 | 96 | |||||
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Multiple Correlation Function Tool Resource Report Resource Website |
Multiple Correlation Function Tool (RRID:SCR_002321) | Multiple Correlation Function Tool | simulation software, software application, software resource | Software tool that provides a convenient environment to simulate NMR diffusion in closed pores. It builds on the eigenfunction expansion of the magnetization. | matlab, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD/MIT-Style Open unspecified license License | nlx_155670 | SCR_002321 | 2026-08-04 09:40:37 | 0 | ||||||||
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MisterI Resource Report Resource Website 1+ mentions |
MisterI (RRID:SCR_002317) | Mr. I, Mr I | data processing software, software resource, software application, image processing software, data visualization software | A powerful and modular medical image viewer/editor. It should be particularly useful to Undergraduates, Postdocs and Researchers in Medical Imaging to visualize data and to easily make attractive figures (for papers or presentations). It will also in a near future offer a number of advanced algorithms for medical image processing. Look at the video to get an idea ! http://www.benoitscherrer.com/MisterI/videos.html | c++, mgh/mgz, magnetic resonance, nifti, nrrd, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Cardware, Http://www.nitrc.org/include/glossary.php#697 | nlx_155666 | SCR_002317 | 2026-08-04 09:40:37 | 1 | ||||||||
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Microstructural correlation toolbox Resource Report Resource Website |
Microstructural correlation toolbox (RRID:SCR_002316) | MSC | software toolkit, software resource, software library | A Matlab-based software library to perform independent component analysis on group white matter skeleton generated by FSL TBSS. The script produces stable estimates of the white matter tract or tract segments that resemble highly correlated variation profiles across a group of subjects. | magnetic resonance, matlab, independent component analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at San Francisco; California; USA |
UCSF NCL Software License | nlx_155665 | SCR_002316 | 2026-08-04 09:40:36 | 0 | ||||||||
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MIAS Registration Toolkit Resource Report Resource Website |
MIAS Registration Toolkit (RRID:SCR_002312) | MIAS Toolkit | data processing software, registration software, software resource, software application, image analysis software | Software toolkit that provides the following libraries and functions on linux platform: # Multi-resolution registration of MR images include T1, multimodality, and DTI images. # The registration model is B-spline, and users can custermize their own image similarity measures by writing a plugin function and recompile the program. | magnetic resonance, dti, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | MIAS license, Http://www.nitrc.org/include/glossary.php#696 | nlx_155659 | SCR_002312 | 2026-08-04 09:40:36 | 0 | ||||||||
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Cognitive Paradigm Ontology Resource Report Resource Website 1+ mentions |
Cognitive Paradigm Ontology (RRID:SCR_002235) | CogPO | ontology, data or information resource, controlled vocabulary | Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. | functional neuroimaging, owl, cognition, behavior |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: BioPortal is related to: Human Imaging Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA has parent organization: Mind Research Network |
NIMH 1R01MH084812-01A1 | Free, Freely available | nlx_155537 | http://www.nitrc.org/projects/cogpo | SCR_002235 | 2026-08-04 09:40:35 | 9 | ||||||
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BrainVision Analyzer Resource Report Resource Website 100+ mentions |
BrainVision Analyzer (RRID:SCR_002356) | BVA | data processing software, software application, software resource, data analysis software | Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more. | Brain Products GmbH, neurophysiology, manage, data, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Products |
Commercially available | nlx_155717 | http://www.nitrc.org/projects/bva | SCR_002356 | BrainVision Analyzer, BrainVision Analyzer 2 | 2026-08-04 09:40:37 | 449 | ||||||
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RT Image Resource Report Resource Website 10+ mentions |
RT Image (RRID:SCR_002535) | RT_Image | software application, software resource | Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data. | computed tomography, magnetic resonance, optical imaging, pet, spect, mri, dicom |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford University School of Medicine; California; USA |
PMID:17375973 | Free, Available for download, Freely available | nlx_155940 | http://www.nitrc.org/projects/rt_image | SCR_002535 | 2026-08-04 09:40:40 | 10 | ||||||
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ROBEX Resource Report Resource Website 1+ mentions |
ROBEX (RRID:SCR_002534) | ROBEX | segmentation software, data processing software, software resource, software application, image processing software, image analysis software | An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts. | magnetic resonance, mri, skull stripping, classification, segmentation, brain, skull | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:21880566 | Free, Available for download, Freely available | nlx_155939 | http://www.nitrc.org/projects/robex | SCR_002534 | Robust Brain Extraction (ROBEX), Robust Brain Extraction | 2026-08-04 09:40:41 | 3 | |||||
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REX Resource Report Resource Website 10+ mentions |
REX (RRID:SCR_002532) | REX | data processing software, software resource, software application, image analysis software, software toolkit | A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial. | analyze, linux, macos, matlab, magnetic resonance, nifti, posix/unix-like, time domain analysis, visualization, workflow, region of interest, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center is related to: Biositemaps |
Free, Available for download, Freely available | nlx_155937 | http://www.nitrc.org/projects/rex | http://www.neuroimaging.org.au/nig/rex | SCR_002532 | 2026-08-04 09:40:40 | 40 | ||||||
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NeuroImaging Analysis Kit (NIAK) Resource Report Resource Website |
NeuroImaging Analysis Kit (NIAK) (RRID:SCR_002497) | NIAK | data processing software, software resource, software application, image processing software, software library, software toolkit | Software library of modules and pipelines for fMRI processing with Octave or Matlab(r) that can run in parallel either locally or in a supercomputing environment. Linux OS and MINC file format are supported. NIAK currently includes a preprocessing, a region growing and a connectome pipelines. NIAK features powerful pipeline management capabilities, including parallel computing, generation of detailed logs and automatic handling of pipeline failures or updates. | reusable library, artifact removal, console (text based), constrained region growing, filtering, frequency domain, image-to-image, image-to-template, independent component analysis, intensity non-uniformity correction, intensity operations, intermodal, intrasubject, linear, matlab, minc, minc2, magnetic resonance, perl, posix/unix-like, principal component analysis, quality metrics, region growing, registration, regression, resampling, segmentation, spatial transformation, statistical operation, workflow, fmri, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155894 | http://www.nitrc.org/projects/niak | SCR_002497 | Neuroimaging Analysis Kit for Matlab and Octave | 2026-08-04 09:40:39 | 0 | ||||||
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R-package for adaptive DWI analysis Resource Report Resource Website |
R-package for adaptive DWI analysis (RRID:SCR_002528) | R-package for adaptive DWI analysis | data processing software, software application, image processing software, software resource | The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, diffusion weighted, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155934 | SCR_002528 | 2026-08-04 09:40:41 | 0 | ||||||||
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Source Information Flow Toolbox Resource Report Resource Website 1+ mentions |
Source Information Flow Toolbox (RRID:SCR_002561) | SIFT | segmentation software, data processing software, software resource, software application, image analysis software, data visualization software, software toolkit | A GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals (EEG, ECoG, MEG, etc), preferably after transforming signals into the source domain. The toolbox consists of four modules: (1) Data Preprocessing, (2) Model Fitting and Connectivity Estimation, (3) Statistical Analysis, (4) Visualization, with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling (AMVAR) algorithms, including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate (in the time-frequency domain) a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time, frequency and anatomical source location. | connectivity analysis, directed transfer analysis, eeg, meg, electrocorticography, granger causality, partial directed coherence |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Swartz Center for Computational Neuroscience |
Free, Available for download, Freely available | nlx_155967 | http://www.nitrc.org/projects/sift | SCR_002561 | 2026-08-04 09:40:42 | 3 | |||||||
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Brain lesion segmentation tool using SVM Resource Report Resource Website |
Brain lesion segmentation tool using SVM (RRID:SCR_002583) | Brain lesion segmentation tool using SVM | segmentation software, data processing software, software resource, software application, image analysis software | Segmentation tool that uses image analysis and machine learning techniques (Support Vector Machines). Image intensities from multiple MR acquisition protocols, after coregistration, are used to form a voxel-wise attribute vector which is used to perform the segmentation. Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency, in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response. | magnetic resonance, brain lesion, image analysis, machine learning, support vector machine |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:23303595 | Free, Available for download, Freely available | nlx_155988 | SCR_002583 | Brain lesion segmentation tool using Support Vector Machines | 2026-08-04 09:40:41 | 0 | ||||||
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Fast Nonlocal Means for MRI denoising Resource Report Resource Website |
Fast Nonlocal Means for MRI denoising (RRID:SCR_002586) | Fast Nonlocal Means for MRI denoising | data processing software, software application, image processing software, software resource | A fast and robust software implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image. It can reach an acceleration factor of 20x over the original implementation, with an improved performance for medium-low SNR images. They use a bias correction step for Rician noise based on the well-known Conventional Approach. This software can be compiled either as a Slicer module or a stand-alone: http://www.nitrc.org/snapshots.php?group_id=518 | analyze, artifact removal, c++, filtering, frequency domain, intensity non-uniformity correction, intensity operation, linux, macos, microsoft, minc, magnetic resonance, nifti, nrrd, other unix-like, posix/unix-like, quality metrics, spatial transformation, nonlocal means, nlm, c++, itk, mri, denoising |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer |
Free, Available for download, Freely available | nlx_155991 | SCR_002586 | 2026-08-04 09:40:42 | 0 | ||||||||
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vis: SPM Visualized Statistics toolbox Resource Report Resource Website 1+ mentions |
vis: SPM Visualized Statistics toolbox (RRID:SCR_002619) | vis | data processing software, software resource, software application, image analysis software, software toolkit | Simple, menu-driven software toolbox for SPM 5/8 for exploratory data analysis for functional or structural images (.img / .nii) provides the user with several options: # a histogram of all non-zero voxel values in a brain image; # a scatter plot, Q-Q plot, or Bland-Altman plots comparing two images; # a surface plot of all voxel values at a particular axial slice; # easy Region of Interst (ROI)-based extraction of voxel values. Note: the toolbox calls various SPM 5/8 functions. The Q-Q plot function requires the MATLAB stats toolbox. | analyze, magnetic resonance, nifti, quantification, statistical operation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: National University of Singapore; Singapore; Singapore |
Free, Available for download, Freely available | nlx_156024 | http://www.nitrc.org/projects/vis | SCR_002619 | Visualized Statistics toolbox (vis), Visualized Statistics toolbox, vis: visualized statistics toolbox | 2026-08-04 09:40:42 | 3 | ||||||
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NFT Resource Report Resource Website 1+ mentions |
NFT (RRID:SCR_002450) | NFT | segmentation software, data processing software, software resource, software application, image analysis software, software toolkit | A MATLAB Toolbox for generating realistic head models from available data (MRI and/or electrode locations), for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic resonance (MR) images. The Boundary Element Method (BEM) and Finite Element Method (FEM) are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line. | eeg, meg, electrocorticography, eeg modeling, forward - inverse, modeling, matlab, mri, electrode |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Swartz Center for Computational Neuroscience |
PMID:20457183 | Free, Available for download, Freely available | nlx_155823 | http://www.nitrc.org/projects/nft | SCR_002450 | NFT: Neuroelectromag Forward Modeling, Neuroelectromagnetic Forward Modeling Toolbox, Neuroelectromagnetic Forward Head Modeling Toolbox | 2026-08-04 09:40:38 | 1 | |||||
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XCEDE Schema Resource Report Resource Website 1+ mentions |
XCEDE Schema (RRID:SCR_002571) | XCEDE | software application, software resource, data management software | Data management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit. | computed tomography, eeg, meg, electrocorticography, magnetic resonance, pet, spect, schema, metadata, neuroimaging, clinical neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Imaging Database |
PMID:21479735 | Free, Available for download, Freely available | nlx_155974 | http://www.xcede.org/XCEDE.html, http://www.nitrc.org/projects/qa_procedure, http://www.nitrc.org/projects/xcede | SCR_002571 | XML-Based Clinical Experiment Data Exchange Schema | 2026-08-04 09:40:41 | 2 |
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