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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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COST Resource Report Resource Website 1000+ mentions |
COST (RRID:SCR_014098) | COST | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:20 | 4519 | |||||||||
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BROCCOLI Resource Report Resource Website 10+ mentions |
BROCCOLI (RRID:SCR_014093) | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:20 | 21 | |||||||||
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3dsvm Resource Report Resource Website |
3dsvm (RRID:SCR_014083) | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:19 | 0 | |||||||||
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BrainCSI Resource Report Resource Website 1+ mentions |
BrainCSI (RRID:SCR_013244) | BrainCSI | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:10 | 1 | |||||||
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NTU-DSI-122: a DSI template in ICBM-152 space Resource Report Resource Website 1+ mentions |
NTU-DSI-122: a DSI template in ICBM-152 space (RRID:SCR_014155) | radiographic image, map, data or information resource, image | A diffusion spectrum imaging (DSI) template constructed in the standard ICBM-152 space from 122 healthy adults. The template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets, rendering it to achieve a high anatomical matching to the ICBM-152 space. This template can serve as a representative DSI dataset for a healthy adult population. It is released in its original DWI format. | dsi, template, map, image, human brain | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:26095830 | Public, Available to the research community | SCR_014155 | 2026-08-04 09:43:21 | 1 | |||||||||
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FastICA Resource Report Resource Website 100+ mentions |
FastICA (RRID:SCR_013110) | FastICA | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:08 | 185 | |||||||
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DTI Atlas Builder Resource Report Resource Website 1+ mentions |
DTI Atlas Builder (RRID:SCR_013112) | DTIAtlasBuilder | data processing software, software application, 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 | 2026-08-04 09:43:08 | 2 | |||||||
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Region to Region Resource Report Resource Website 1+ mentions |
Region to Region (RRID:SCR_016995) | data processing software, software application, software resource | Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another. | connectivity, pattern, region, neuroinformatics, region, receptive, field, model, visual, neuroscience, voxel, mapping, 3D, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Stony Brook University; New York; USA |
Free, Available for download, Freely available | SCR_016995 | 3-D Connective Field Modeling Toolbox | 2026-08-04 09:44:04 | 1 | |||||||||
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HeuDiConv: a heuristic-centric DICOM converter Resource Report Resource Website 10+ mentions |
HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) | HeuDiConv | data processing software, software application, software resource | Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts. | Flexible, DICOM, converter, organizing, brain, image, data, structured, directory, layout | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | http://www.nitrc.org/projects/heudiconv/ | SCR_017427 | heudiconv, heuristic-centric DICOM converter | 2026-08-04 09:44:13 | 28 | ||||||||
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Longitudinal MS Lesion Imaging Archive Resource Report Resource Website |
Longitudinal MS Lesion Imaging Archive (RRID:SCR_014136) | data set, data or information resource, 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 | 2026-08-04 09:43:20 | 0 | |||||||||
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NITRC Community Conferences Workshops and Meetings Resource Report Resource Website |
NITRC Community Conferences Workshops and Meetings (RRID:SCR_002323) | Conferences Workshops and Meetings | workshop, training resource, meeting resource | Project to assist the community in the support of information about upcoming Conferences, Workshops and Meetings. Such support may be documents, news, files, etc. To see a listing of upcoming Events, please use the NITRC Community Events Page at http://www.nitrc.org/incf/event_list.php (and tab at right). To announce an Event, please use the Submit an Event at the NITRC Community Events Page, http://www.incf.org/Events/events/createObject?type_name=Event (and tab at right). Note, INCF account is currently required. All users are encouraged to check this site for upcoming meetings, and promote future meetings here. | knowledge environment, os independent, conference, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
The community can contribute to this resource, Account required | nlx_155672 | SCR_002323 | NITRC / INCF Community Conferences Workshops and Meetings | 2026-08-04 09:40:36 | 0 | |||||||
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medInria Resource Report Resource Website 50+ mentions |
medInria (RRID:SCR_001462) | data processing software, registration software, software resource, software application, image processing software, software library, image analysis software, data visualization software, software toolkit | Software tool as multi platform medical image processing and visualization software. Functionalities include 2D/3D/4D image visualization, image registration, diffusion MR processing and tractography, filtering. | Magnetic resonance, image visualization, image registration, diffusion mr processing, tractography, diffusion tensor mri, fmri, mri, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: National Institute for Research in Computer Science and Control; Brittany; France |
Free, Available for download, Freely available | nif-0000-00292 | http://www.nitrc.org/projects/medinria | SCR_001462 | 2026-08-04 09:40:23 | 77 | ||||||||
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NiLearn Resource Report Resource Website 100+ mentions |
NiLearn (RRID:SCR_001362) | NiLearn | data processing software, software resource, software application, image processing software, software library, software toolkit | A software package to facilitate the use of statistical learning on NeuroImaging data. Namely NiLearn leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis. | analyze, clinical neuroinformatics, magnetic resonance, nifti, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
Free, Freely Available | nlx_155897 | http://www.nitrc.org/projects/nilearn | SCR_001362 | NiLearn: Machine learning for Neuro-Imaging in Python | 2026-08-04 09:40:21 | 434 | ||||||
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aBEAT Resource Report Resource Website 1+ mentions |
aBEAT (RRID:SCR_002238) | aBEAT | data processing software, software resource, software application, image processing software, image analysis software, software toolkit | A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing. | analyze, atlas application, magnetic resonance, segmentation, visualization, adult, mri, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:23577105 | nlx_155840, nlx_155542 | http://www.nitrc.org/projects/abeat | SCR_002238 | aBEAT: A Toolbox for Consistent Analysis of Longitudinal Adult Brain MRI, Adult Brain Extraction and Analysis Toolbox | 2026-08-04 09:40:36 | 1 | ||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | simulation software, data processing software, software resource, software application, data visualization software, software toolkit | A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6. | modeling, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BioMesh3D is related to: BioMesh3D is related to: BioPSE is related to: BioPSE has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
Free, Available for download, Freely available | nlx_155949 | http://www.nitrc.org/projects/scirun | SCR_002541 | 2026-08-04 09:40:40 | 21 | ||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | data processing software, software resource, software application, image processing software, image analysis software, software toolkit | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-08-04 09:40:48 | 27070 | ||||
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R-package for adaptive fMRI analysis Resource Report Resource Website |
R-package for adaptive fMRI analysis (RRID:SCR_002530) | R-package for adaptive fMRI analysis | data processing software, software resource, software application, image processing software, image analysis software | The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155935 | SCR_002530 | 2026-08-04 09:40:40 | 0 | ||||||||
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MRI Defacer Resource Report Resource Website |
MRI Defacer (RRID:SCR_002424) | mri_deface | data processing software, software application, image processing software, software resource | Tool to remove facial features from an MRI structural image for the purpose of de-identification. | console (text based), intensity operations, linux, macos, mgh/mgz, magnetic resonance, posix/unix-like, resampling, spatial transformation, surface analysis, hipaa, data sharing, de-identification | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155798 | http://www.nitrc.org/projects/mri_deface | SCR_002424 | mri deface | 2026-08-04 09:40:39 | 0 | ||||||
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LONI ShapeTools Resource Report Resource Website 1+ mentions |
LONI ShapeTools (RRID:SCR_002697) | ShapeTools | software development tool, software resource, software application, software library, software toolkit | Software library that is a collection of Java classes that enable Java programmers to model, manipulate and visualize geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines. * File format readers that implement ShapeIO interface (modeled after Java ImageIO) are automatically used when appropriate. * Storage of additional metadata of arbitrary type (other than shape vertices and interconnections) is enabled by the use of data attributes. * Shapes may contain a set of child shapes allowing for the construction and manipulation of complex hierarchies of shapes. * The various components of a shape are specified as interfaces with specific implementations, making it easy to create specialized implementations of a shape component when different performance characteristics are required. | data visualization, java, shape analysis software, computed tomography, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: LONI ShapeViewer has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
Free, Freely available | nif-0000-23323 | SCR_002697 | 2026-08-04 09:40:43 | 1 | |||||||
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GEneral NEural SImulation System: The Neurospaces Project Resource Report Resource Website 1+ mentions |
GEneral NEural SImulation System: The Neurospaces Project (RRID:SCR_008035) | simulation software, portal, topical portal, software resource, software application, data or information resource | The GEneral NEural SImulation System (GENESIS) started as a very advanced software package in the late eighties, for biologically accurate neuronal modeling. Besides being used as a neuronal simulator, it was also applied to various domains outside computational neuroscience. The Neurospaces project is a departure from the monolithic software system design of the original GENESIS system. It is a development center for software components of computational neuroscience simulators. There are many advantages of developing independent software components: - Interfacing to an individual component is obviously more simple than interfacing to a do-all monolithic system. The compartmental solver developed for the Neurospaces project can be connected to Matlab fi. - It simplifies the individual components and encourages other developers to get involved. - It allows for separate testing of the components. More than 1000 use case tests been defined for these software components, including integration tests. - Integrating different component, gives different flavours of the same simulator, and enhances the user experienced consistency when doing multilevel simulations. - A component based software system avoids vendor-lockin. Its life-cycle is more smooth than that of a monolithic system, because software components can be upgraded one at a time. The Neurospaces project embodies many software components that all have been developed in full isolation. The core of the most important components is finished. The current development focus has shifted from component integration to the support of specific use case with an emphasis on single neuron modeling. This is a list of software components that have been developed or are under construction. Together, these tools give the core for the upcoming GENESIS 3 GUI. - GShell: a simple replacement for the Genesis 2 SLI. - Heccer: a fast compartmental solver, a backend. - Dash: a second compartmental solver faster than Heccer, for simpler models. - Neurospaces Model Container: provides a solver independent internal and external storage format for models. - Discrete event system: consists of a discrete event distributor and queuer. This is used for abstract modeling of an action potential traveling inside an axon as a ''discrete event''. - SSP: a flexible scheduler written in perl, to run simulations with the Neurospaces model container and Heccer. - The Neurospaces Studio: some tools for graphical browsing and command line usage. - The Genesis Script Language Interface: a scripting component that reads Genesis 2 scripts and feeds them to the Neurospaces model container. - The Geometry Library is a general purpose geometry library, with some essential geometrical operators, not commonly found in other geometrical libraries. - Using the Geometry Library, a Reconstruct Interface has been written. This interface supports the conversion of contours exported by the Reconstruct software to the Neurospaces declarative NDF format. - The Neurospaces project browser for browsing projects and inspecting simulation results. - The Installer package contains the Neurospaces installer and developer tools that have emerged from developing Neurospaces software components. - The Configurator package contains configuration utilities for the other tools. It is not needed for the other tools to work properly. Rather, it allows to set up model database and simulation servers in a convenient way. - There is also a Neurospaces blog and a wiki at googlecode for the Neurospaces project, with information for developers. | action potential, biologically, cell, computational, development, interface, mathematical, memory, model, modeling, neural, neuron, neuronal, neuroscience, physics, scripting, simulation, simulator, software, database |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Texas at San Antonio; Texas; USA |
nif-0000-10233 | SCR_008035 | GENESIS Neurospaces | 2026-08-04 09:42:05 | 2 |
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