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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CURRY Resource Report Resource Website 100+ mentions |
CURRY (RRID:SCR_009546) | CURRY | software application, data processing software, software resource | Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package. | multimodal, atlas, application, connectivity, analysis, computed, tomography, database, eeg, meg, electrocorticography, modeling, finite, element, format, conversion, forward, inverse, image, reconstruction, meg, mesh, generation, model, magnetic resonance, pet, spect, segmentation, simulation, spatial, transformation, volumetric, neuroimaging, FASEB list | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155726 | http://www.nitrc.org/projects/curry_7 | SCR_009546 | CURRY Scan 7 Neuroimaging Suite, CURRY 8, CURRY 7, CURRY Neuroimaging Suite | 2026-08-10 09:33:44 | 170 | ||||||
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COST Resource Report Resource Website 1000+ mentions |
COST (RRID:SCR_014098) | COST | software application, image analysis software, data processing software, software resource | A tool that implements a graph-based connectivity assessment method. This method uses a multi-directional graph propagation method applied to sampled orientation distribution function (ODF), which can be computed directly from the original diffusion imaging data. | software tool, connectivity assessment, image analysis software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
SCR_014098 | Connectivity Orientation Spherical distribution Tool | 2026-08-10 09:34:57 | 4543 | |||||||||
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BROCCOLI Resource Report Resource Website 10+ mentions |
BROCCOLI (RRID:SCR_014093) | software application, image analysis software, data processing software, software resource | A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations. | software package, parallel analysis, fmri, non linear spatial normalization, brain | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | https://github.com/wanderine/BROCCOLI/ | SCR_014093 | 2026-08-10 09:34:57 | 22 | |||||||||
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3dsvm Resource Report Resource Website |
3dsvm (RRID:SCR_014083) | software application, image analysis software, data processing software, software resource | A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. | plugin, afni, svm light, support vector machine, image analysis software |
uses: Analysis of Functional NeuroImages is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Public | http://www.nitrc.org/projects/afni_3dsvm | SCR_014083 | 2026-08-10 09:34:57 | 0 | |||||||||
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BrainCSI Resource Report Resource Website 1+ mentions |
BrainCSI (RRID:SCR_013244) | BrainCSI | software application, image analysis software, data processing software, software resource | A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images. | magnetic resonance spectroscopy, c++, console (text based), dicom, macos, microsoft, magnetic resonance, nifti, posix/unix-like, software, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
BSD License | nlx_155711 | http://www.nitrc.org/projects/braincsi | SCR_013244 | 2026-08-10 09:34:44 | 1 | |||||||
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FastICA Resource Report Resource Website 100+ mentions |
FastICA (RRID:SCR_013110) | FastICA | software application, image analysis software, data processing software, software resource | General-purpose unsupervised data-analysis tool, most often used for brain imaging data. | independent component analysis, magnetic resonance, statistical operatio, matlab |
is used by: ICASSO is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Aalto University; Espoo; Finland |
GNU General Public License | nlx_155758 | http://www.nitrc.org/projects/incf_fastica | SCR_013110 | 2026-08-10 09:34:49 | 200 | |||||||
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DTI Atlas Builder Resource Report Resource Website 1+ mentions |
DTI Atlas Builder (RRID:SCR_013112) | DTIAtlasBuilder | software application, data processing software, software resource | This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work, so be sure to have these installed on your computer: - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher If you download the package, be sure to have the glut library installed. | magnetic resonance, dti, atlas | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155738 | http://www.nitrc.org/projects/dtiatlasbuilder | SCR_013112 | 2026-08-10 09:34:42 | 2 | |||||||
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Longitudinal MS Lesion Imaging Archive Resource Report Resource Website |
Longitudinal MS Lesion Imaging Archive (RRID:SCR_014136) | data or information resource, data set, image collection | The Longitudinal MS Lesion Imaging Archive provides Training data consisting of longitudinal images from five patients and Testing data consisting of 15 patients. Each longitudinal dataset includes T1-weighted, T2-weighted, PD-weighted, and T2-weighted FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. T1-weighted images have approximately a 1mm cubic voxel resolution, while the other scans are 1mm in plane with 3mm sections. Accounting for the multiple time points, this constitutes approximately 80 individual data sets. The Training data contains manual segmentations of the MS lesions from two different raters for each of the time points provided. | data set, image collection, longitudinal image, t1 weighted, t2 weighted |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
http://www.iacl.ece.jhu.edu/MSChallenge | SCR_014136 | Longitudinal MS Lesion Segmentation Challenge | 2026-08-10 09:34:57 | 0 | |||||||||
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Connectir Resource Report Resource Website 1+ mentions |
Connectir (RRID:SCR_000863) | Connectir | software application, image analysis software, data processing software, software resource | An R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity. | console (text based), magnetic resonance, r, connectivity, brain, connectome-wide association study, functional connectivity | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155729 | http://www.nitrc.org/projects/connectir | SCR_000863 | 2026-08-10 09:31:16 | 1 | |||||||
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Net Station API Resource Report Resource Website |
Net Station API (RRID:SCR_000867) | Net Station API | data access protocol, commercial organization, application programming interface, software resource | APIs for Net Station data files. APIs are available for C++, C#, and Java. | eeg, meg, electrocorticography, c++, java, visualization, analysis, presentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Net Station EEG Software |
Free, Available for download, Freely available | nlx_155824 | http://www.nitrc.org/projects/netstation_api | SCR_000867 | Net Station Software for EEG Acquisition and Physician and Review | 2026-08-10 09:31:16 | 0 | ||||||
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PyMVPA Resource Report Resource Website 100+ mentions |
PyMVPA (RRID:SCR_006099) | PyMVPA | software application, software toolkit, software resource | A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. | python, machine learning, fmri, eeg, neuroimaging, image analysis, scripting, multivariate pattern analysis, brain, meg, extracellular recording, algorithm, reusable library, analyze, c, console (text based), eeg, meg, electrocorticography, frequency domain, independent component analysis, linear, modeling, magnetic resonance, multivariate analysis, nifti, nonlinear, os independent, pet, spect, principal component analysis, python, regression, spatial transformation, statistical operation, temporal transformation, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: neurodebian is related to: CoSMoMVPA has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
German Academic Exchange Service PPP-USA D/05/504/7; NIMH MH080526; NSF SBE 0751008; James McDonnell Foundation 220020127 |
PMID:19184561 PMID:19212459 PMID:20582270 |
MIT License | nlx_151596 | http://www.nitrc.org/projects/pymvpa | SCR_006099 | Python MVPA, Multivariate Pattern Analysis in Python, PyMVPA - Multivariate Pattern Analysis in Python | 2026-08-10 09:32:44 | 144 | ||||
|
BRAINSCortex Resource Report Resource Website |
BRAINSCortex (RRID:SCR_001082) | BRAINSCortex | software application, software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature. | analyze, application, c++, console (text based), linux, macos, microsoft, morphology, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, brain. surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: INCF Software Center has parent organization: BRAINSTools |
Free, Available for download, Freely available | nlx_155698 | http://www.nitrc.org/projects/brainscortex | SCR_001082 | 2026-08-10 09:31:20 | 0 | |||||||
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INCF Software Center Resource Report Resource Website 1+ mentions |
INCF Software Center (RRID:SCR_002347) | INCF Software Center | software repository, software resource | Software repository that makes it easy for neuroscientists to find, use and share software tools. The Software Center is accessible to everyone: you can browse and download available software tools without registering. However, by creating an account, you will be able to post comments, and request to join development teams. The INCF Software Center and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are sharing content. Software tools hosted by NITRC also appear at the INCF Software Center. Your software tool will be available to all users of the Software Center. You will be able to upload documentation, executables and related files; track use of your software; create a wiki; and establish a development team. Registered Software Center users will be able to comment on and post reviews about your software, and can request to join your development team. INCF's vision of the Software Center is that it will become a communication enabler for software users as well as developers. Accordingly, future system features to be added include communication and collaboration functions. We also plan to include support services to allow software developers organize their software, track the use, and receive feedback for further improvement and development. Further development of the Software Center will be strongly driven by the user needs. Please let us know what features you would like to see added. | neuroscience, software, database |
lists: 3DSlicerLupusLesionModule lists: BRAINSCut lists: BRAINSCortex lists: Sumatra is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VectorValuedHistogramNormalizer is related to: NITRC Community Conferences Workshops and Meetings is related to: Automatic Segmentation Tool Adapter is related to: R-package for adaptive DWI analysis is related to: R-package for adaptive fMRI analysis is related to: REX is related to: SPHARM-PDM Toolbox is related to: Brain lesion segmentation tool using SVM is related to: UNC Human Brain Atlas is related to: ValMap: simple statistical mapping tool is related to: DW-MRI Random Walk Simulator is related to: NeuronVisio is related to: Brainvox is related to: JIST Resources for Algorithm Development is related to: BRAINSDemonWarp is related to: BrainMask Volume Processing Tool is related to: DTI BrainImageScope is related to: ProbabilisticBiasCorrection is related to: BrainCSI is related to: Slicer3 Example Modules is related to: TOADS-CRUISE Brain Segmentation Tools is related to: ABC (Atlas Based Classification) is related to: Whole Brain Catalog is related to: BrainVisa Morphology extensions has parent organization: International Neuroinformatics Coordinating Facility is parent organization of: PANDORA Matlab Toolbox |
The community can contribute to this resource | nif-0000-00372 | SCR_002347 | International Neuroinformatics Coordinating Facility Software Center | 2026-08-10 09:31:42 | 8 | |||||||
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CAMINO-TRACKVIS Resource Report Resource Website |
CAMINO-TRACKVIS (RRID:SCR_009450) | CAMINO-TRACKVIS | systems interoperability software, software application, software resource | Software package that allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital. With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts. | magnetic resonance, tractography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Camino is related to: TrackVis |
MIT License, X Consortium License | nlx_155594 | SCR_009450 | 2026-08-10 09:33:42 | 0 | ||||||||
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FSL extensions Resource Report Resource Website 1+ mentions |
FSL extensions (RRID:SCR_009472) | FSL extensions | software repository, software resource | A reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL |
nlx_155619 | SCR_009472 | 2026-08-10 09:33:42 | 2 | |||||||||
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fMRI Artefact rejection and Sleep Scoring Toolbox Resource Report Resource Website 10+ mentions |
fMRI Artefact rejection and Sleep Scoring Toolbox (RRID:SCR_009620) | FASST | software application, software toolkit, software resource | An EEG toolbox developed to help users with 3 specific types of data and problems: simulatenous EEG-fMRI recording, continuous EEG scoring (e.g. sleep) and handling (visualisation, cutting, power spectrum, etc.) multi-channel recording of spontaneous EEG. The toolbox is written in Matlab and is specifically compatible with the BrainAmp family of EEG recorders (from BrainProducts GmbH) Three other data formats are now also supported: the edf "European Data Format", exported raw-EGI data (from Electrical Geodesics, Inc.) and the BCI2000 format.The results are directly compatible with SPM8 and are saved with SPM8 EEG data format. | eeg, meg, electrocorticography, matlab, magnetic resonance, os independent, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Liege; Wallonia; Belgium |
PMID:21461381 | GNU General Public License | nlx_155846 | http://www.nitrc.org/projects/fasst | SCR_009620 | FASST - fMRI Artefact rejection and Sleep Scoring Toolbox | 2026-08-10 09:33:45 | 18 | |||||
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DICOMConvert Resource Report Resource Website |
DICOMConvert (RRID:SCR_014100) | software application, standalone software, software resource | A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd). | standalone software, dicom, image converter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
Center for Infectious Disease Imaging ; NIAID ; NIBIB |
Available for download | SCR_014100 | Dicom Converter | 2026-08-10 09:34:57 | 0 | ||||||||
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Notion ResearchPACS Resource Report Resource Website |
Notion ResearchPACS (RRID:SCR_014154) | software application, standalone software, software resource | Standalone software designed to be used by radiology researchers for storage and anonymization of research images. | standalone software, radiology, storage, research image, anonymization, pacs | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014154 | 2026-08-10 09:34:58 | 0 | ||||||||||
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Hitachi Optical Topography System Resource Report Resource Website |
Hitachi Optical Topography System (RRID:SCR_000865) | Hitachi Optical Topography System | instrument supplier, material resource | 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 | 2026-08-10 09:31:16 | 0 | |||||||
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NIRx NIRS Neuroimaging Resource Report Resource Website 10+ mentions |
NIRx NIRS Neuroimaging (RRID:SCR_002491) | instrument supplier, material resource | 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 | 2026-08-10 09:31:44 | 21 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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