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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BrainCSI Resource Report Resource Website 1+ mentions |
BrainCSI (RRID:SCR_013244) | BrainCSI | data processing software, image analysis software, software application, 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 | 2026-09-19 12:56:02 | 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) | data or information resource, image, map, radiographic 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 | 2026-09-19 12:56:02 | 1 | |||||||||
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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 | 2026-09-19 12:56:06 | 2 | |||||||||
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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 | 2026-09-19 12:56:07 | 34 | ||||||||
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SCIRun Resource Report Resource Website 10+ mentions |
SCIRun (RRID:SCR_002541) | SCIRun | data processing software, data visualization software, simulation software, software application, software resource, 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 | 2026-09-19 12:55:05 | 22 | ||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | data processing software, image analysis software, image processing software, software application, software resource, 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 |
NIGMS RC2 GM092519; NIH ; NIMH ; NINDS ; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; Wellcome Trust Strategic Award 095931 |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, SCR_018407, nif-0000-30467 | 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 | 2026-09-19 12:55:06 | 29025 | ||||
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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, image analysis software, image processing software, software application, software resource | 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 | 2026-09-19 12:55:05 | 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 | meeting resource, training resource, workshop | 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 | 2026-09-19 12:55:05 | 0 | |||||||
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MRI Defacer Resource Report Resource Website |
MRI Defacer (RRID:SCR_002424) | mri_deface | data processing software, image processing software, software application, 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 | 2026-09-19 12:55:05 | 0 | ||||||
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LONI ShapeTools Resource Report Resource Website 1+ mentions |
LONI ShapeTools (RRID:SCR_002697) | ShapeTools | software application, software development tool, software library, software resource, 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 | 2026-09-19 12:55:05 | 1 | |||||||
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aBEAT Resource Report Resource Website 1+ mentions |
aBEAT (RRID:SCR_002238) | aBEAT | data processing software, image analysis software, image processing software, software application, software resource, 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 | 2026-09-19 12:55:04 | 1 | ||||||
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ArtRepair for robust fMRI Resource Report Resource Website 100+ mentions |
ArtRepair for robust fMRI (RRID:SCR_005990) | ArtRepair | data processing software, data visualization software, image analysis software, software application, software resource, software toolkit | A toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment, data repair, and noise filtering, and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data, including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change. * Operating System: OS Independent * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 * execution requires: SPM | algorithm or reusable library, artifact removal, quality metrics, motion analysis, image display, fmri, motion adjustment, data repair, noise filtering, high motion, pediatric, spm, matlab, clinical. pediatric, child |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Stanford University School of Medicine; California; USA |
Acknowledgement required, Non-commercial | nlx_151367 | http://www.nitrc.org/projects/art_repair | SCR_005990 | Art Repair, ArtRepair Software | 2026-09-19 12:55:08 | 118 | ||||||
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Free-D Resource Report Resource Website 10+ mentions |
Free-D (RRID:SCR_009578) | Free-D | data processing software, image analysis software, image reconstruction software, software application, software resource | Free-D allows the reconstruction of 3D models from image stacks (segmentation, registration, surface reconstruction, 3D rendering). It is designed in the goal of non-linear spatial normalization and averaging of collections of individual 3D models (this module is currently in alpha version only and not included in the distributed version)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: INRA - French National Institute for Agricultural Research; Paris; France |
PMID:15922039 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155760 | http://www.nitrc.org/projects/incf_free-d | SCR_009578 | 2026-09-19 12:55:11 | 27 | ||||||
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Diffusional Kurtosis Estimator Resource Report Resource Website 1+ mentions |
Diffusional Kurtosis Estimator (RRID:SCR_009563) | DKE | data processing software, image processing software, software application, software resource | A software tool for post-processing diffusional kurtosis imaging (DKI) datasets. DKE consists of a suite of command-line programs along with a graphical user interface (GUI). DKE is currently supported on 32- and 64-bit Windows platforms. Given a set of diffusion-weighted images acquired following a valid DKI protocol, DKE generates a set of kurtosis (axial, mean, radial) parametric maps. DKE also generates diffusivity (axial, mean, radial) and fractional anisotropy maps using both DKI and diffusion tensor imaging signal models. DKE features include: DICOM and NIfTI format support, interactive (GUI) as well as batch mode (command-line) processing, and rigid-body motion correction. DKE implements the methods described in the following paper: Tabesh A, Jensen JH, Ardekani BA, and Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Mag Reson Med. 2011 Mar;65(3):823-36. http://www.ncbi.nlm.nih.gov/pubmed/21337412 | application, c++, dicom, matlab, microsoft, modeling, magnetic resonance, nifti, quantification, super tensor, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Medical University of South Carolina; South Carolina; USA |
PMID:21337412 | DKE License | nlx_155744 | http://www.nitrc.org/projects/dke | SCR_009563 | 2026-09-19 12:55:11 | 8 | ||||||
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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 | data or information resource, narrative 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 | 2026-09-19 12:55:11 | 0 | |||||||||
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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) | data or information resource, portal, simulation software, software application, software resource, topical portal | 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 | 2026-09-19 12:55:10 | 2 | |||||||||
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CARLsim: a GPU-accelerated SNN Simulator Resource Report Resource Website 1+ mentions |
CARLsim: a GPU-accelerated SNN Simulator (RRID:SCR_014095) | simulation software, software application, software resource | A GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level. | simulation software, snn model, gpu accelerated, library, izhikevich spiking neuron, graphics processor, stdp, data parallelism |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
Available for download | http://www.socsci.uci.edu/~jkrichma/CARLsim/ | SCR_014095 | CARLsim | 2026-09-19 12:55:13 | 4 | ||||||||
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MRIcroS Resource Report Resource Website 1+ mentions |
MRIcroS (RRID:SCR_014142) | data analysis software, data processing software, data visualization software, software application, software resource | A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap. | data visualization software, data analysis software, surface mesh visualization, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Medical University of South Carolina; South Carolina; USA |
Available to the research community | SCR_014142 | 2026-09-19 12:55:13 | 3 | ||||||||||
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Multivariate General Linear Models (MGLM) on Riemannian Manifolds Resource Report Resource Website |
Multivariate General Linear Models (MGLM) on Riemannian Manifolds (RRID:SCR_014143) | data analysis software, data processing software, software application, software resource | A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used. | data analysis software, statistical analysis, ti, spd, odf |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Available to the research community | SCR_014143 | MGLM on Riemannian Manifolds, Multivariate General Linear Models on Riemannian Manifolds | 2026-09-19 12:55:13 | 0 | |||||||||
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GIMME Resource Report Resource Website 1+ mentions |
GIMME (RRID:SCR_014115) | GIMME | data analysis software, data processing software, software application, software resource, software toolkit | Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels. | Functional, connectivity, analysis, fMRI, BOLD, signal, predefined, region, pattern, BRAIN Initiative |
uses: MATLAB is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NIBIB EB022904; NIBIB R21 EB015573; NSF 0852147 |
PMID:22732562 | Free, Available for download, Freely available | SCR_014115 | Group Iterative Multiple Model Estimation | 2026-09-19 12:55:13 | 2 |
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