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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
BrainBrowser
 
Resource Report
Resource Website
1+ mentions
BrainBrowser (RRID:SCR_009535) BrainBrowser service resource, analysis service resource, data or information resource, data analysis service, production service resource, data set A web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface. BrainBrowser has two modes of operation, exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode, the user may choose to explore the correlation structure for cortical thickness, cortical area or cortical volume, or any other pre-calculated metric. In the second mode, the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI, using the same simple file format (.obj) as for surface data. BrainBrowser on Youtube: http://www.youtube.com/watch?v=HlRTUYUf1Ew NOTE: BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability. image display, javascript, minc2, magnetic resonance, nifti, os independent, rendering, ruby, surface rendering, three dimensional display, two dimensional display, visualization, volume rendering, 3d visualization, neuroimaging, fmri, web application, web resource, data visualization service is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: McGill University; Montreal; Canada
Free nlx_155710 http://www.nitrc.org/projects/brainbrowser SCR_009535 2026-08-11 09:41:52 3
Wisconsin White Matter Hyperintensities Segmentation Toolbox
 
Resource Report
Resource Website
1+ mentions
Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) W2MHS software application, software toolkit, image analysis software, software resource, software library, segmentation software, data processing software An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis. computational neuroscience, matlab, nifti, white matter hyperintensity, c++, matlab, ms windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: SPM
is related to: SourceForge
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
has parent organization: SourceForge
Alzheimer's disease, Aging, Neurological disorder Academic Free License nlx_156021 SCR_009652 WM Hyperintensities Segmentation Toolbox 2026-08-11 09:41:55 2
BVQXtools
 
Resource Report
Resource Website
10+ mentions
BVQXtools (RRID:SCR_009532) BVQXtools software application, software toolkit, image processing software, software resource, data processing software A Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. The toolbox is freely available. analyze, format conversion, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, statistical operation, time domain analysis, windows, workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: BrainVoyager
Free, Other/Commercial license License nlx_155707 SCR_009532 2026-08-11 09:41:52 11
B0 and eddy current correction for DTI
 
Resource Report
Resource Website
B0 and eddy current correction for DTI (RRID:SCR_009529) B0 and Eddy Current Correction Code for Diffusion MRI source code, data processing software, software resource, software application Software tool (excecutable and source code in C and C++) to correct distortions in diffusion MR images that are generated by main magnetic field inhomogeneities and eddy current induced fields generated from the direction-dependent diffusion encoding analyze, c, c++, microsoft, magnetic resonance, win32 (ms windows), dti, diffusion mri, magnetic field, eddy current is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Biomedical Informatics Research Network
GNU General Public License nlx_155694 http://www.nitrc.org/projects/dtic SCR_009529 2026-08-11 09:41:53 0
BRAINSDemonWarp
 
Resource Report
Resource Website
1+ mentions
BRAINSDemonWarp (RRID:SCR_009524) BRAINSDemonWarp software application, registration software, image analysis software, software resource, data processing software A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: INCF Software Center
has parent organization: University of Iowa; Iowa; USA
NINDS NS050568;
NINDS NS40068;
NIMH MH31593;
NIMH MH40856
nlx_155700 http://www.nitrc.org/projects/brainsdemonwarp SCR_009524 2026-08-11 09:41:52 1
SPM SS - fMRI functional localizers
 
Resource Report
Resource Website
1+ mentions
SPM SS - fMRI functional localizers (RRID:SCR_009644) spm_ss software application, software toolkit, image analysis software, software resource, data processing software Spm-toolbox that performs region of interest (ROI)-level and voxel-level between-subjects analyses of functional MRI data, restricting the analyses to those areas identified using subject-specific functional localizers. Methods: The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics) This toolbox requires Matlab and SPM5/SPM8. analyze, linear, matlab, modeling, magnetic resonance, nifti, os independent, regression, statistical operation, win32 (ms windows), statistical parametric mapping, fmri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: SPM
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
MIT License, X Consortium License nlx_155955 http://www.nitrc.org/projects/spm_ss SCR_009644 spm_ss toolbox, SPM toolbox for subject-specific analyses 2026-08-11 09:41:55 5
GPU based affine registration
 
Resource Report
Resource Website
GPU based affine registration (RRID:SCR_009486) GPU based affine registration software application, registration software, image analysis software, software resource, data processing software This tool can be used as a command line module with 3D Slicer (version 3 and above) for the affine registration of image volumes. The registration toolbox has 2 options: 1) a Mutual Information based registration, 2) a Sum-of-Square differences registration method. The final output is in the same space as the fixed image. You do require to have CUDA v2.2 or greater installed on your system with atleast 256MB Nvidia GPU memmory card. All operating systems are supported, but take a look at the CMakeLists.txt file for how to compile for you system. magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: 3D Slicer
GPL-Style Open unspecified license, Http://www.nitrc.org/include/glossary.php#573 nlx_155633 SCR_009486 2026-08-11 09:41:52 0
fMRI Classification in R
 
Resource Report
Resource Website
1+ mentions
fMRI Classification in R (RRID:SCR_009519) fMRI Classification in R software application, image analysis software, image processing software, software resource, data processing software They demonstrate and provide R code that can classify between groups of fMRI scans based on functional network connectivity differences, requiring only 4 lines of code to be altered. In addition, they include a detailed article explaining the methods behind and motivations of this tool. This code can also be altered to perform connectivity analysis and classification using ROI based methods by reading in distance arrays previously created. They run Independent component analysis (ICA) on fMRI data to establish functional networks, measure the functional connectivity between these networks using the temporal cross-correlations between independent component to create a distance matrix and indicating the networking. Connectivity properties are used as a feature matrix for an SVM classifier. Collectively, this project provides and explains both methods and code to perform functional network connectivity and fMRI SVM classi?cation. magnetic resonance, connectivity, fmri, independent component analysis, functional network, classification is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) GNU General Public License nlx_155681 SCR_009519 2026-08-11 09:41:52 1
Level-set Segmentation for Slicer3
 
Resource Report
Resource Website
Level-set Segmentation for Slicer3 (RRID:SCR_009558) Level-set Segmentation for Slicer3 software application, image analysis software, software resource, segmentation software, data processing software The modules in the framework support different tasks in the segmentation realization in 3DSlicer. A module called Level-set label map evolver was developed, which takes an initial label image and a feature image as input and performs a Geodesic Active Contours evolution on the label image according to the feature image and to a different terms in the level-set equation. The evolution takes place for a customizable number of iterations. The output is a label image that can be used to produce a model. Other modules were developed to accompany the main module as can be seen in http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Level-Set_Segmentation_Framework-Documentation magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: 3D Slicer
3D Slicer License nlx_155786 http://www.nitrc.org/projects/levelsetslicer3 SCR_009558 Slicer3:Module:Level-Set Segmentation Framework 2026-08-11 09:41:53 0
DRAMMS
 
Resource Report
Resource Website
10+ mentions
DRAMMS (RRID:SCR_009555) DRAMMS software application, registration software, image analysis software, software resource, data processing software A software designed for deformable 2D-to-2D and 3D-to-3D image registration. Some typical applications of DRAMMS include, ** Cross-subject registration of the same organ (can be brain, breast, cardiac, etc); ** Mono- and Multi-modality registration (MRI, CT, histology); Longitudinal registration (pediatric brain growth, cancer development, etc); ** Registration under partial missing correspondences (small lesions, tumors, histological cuts). DRAMMS is implemented as a Unix command-line tool. It is fully automatic and easy to use ? users input two images, and DRAMMS will output the registered image and deformation. No need for pre-segmentation of any structures, no need for any prior knowledge, and no need for human initialization or intervention. analyze, computational neuroscience, linux, macos, magnetic resonance, nifti, posix/unix-like, brain morphometry, general registration, image registration is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Pennsylvania; Philadelphia; USA
BSD License nlx_155736 http://www.nitrc.org/projects/dramms SCR_009555 Deformable Registration via Attribute Matching and Mutual-Saliency Weighting, DRAMMS: Deformable Registration via Attribute Matching and Mutual-Saliency Matching 2026-08-11 09:41:53 11
Connectome Viewer
 
Resource Report
Resource Website
1+ mentions
Connectome Viewer (RRID:SCR_009552) Connectome Viewer data analysis software, software application, software toolkit, software resource, data processing software, data visualization software A free, open source, cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include: Connectome File Format including metadata, networks, surfaces, volumes, track files; complex network analysis toolboxes; modular plugin architecture for extensibility; Mayavi2 for 3D Scientific Visualization and Plotting; interactive data manipulation and scripting capabilities; and Neuroimaging and Diffusion in Python libraries. animation, atlas application, c++, format conversion, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, posix/unix-like, python, rendering, software, surface rendering, three dimensional display, tractography, two dimensional display, visualization, volume rendering, win32 (ms windows), windows, connectome, connectomics, data management, multi-modal data, network analysis, neuroimaging is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Connectome Mapping Toolkit
PMID:21713110 Open Source nlx_155732 http://www.nitrc.org/projects/cviewer SCR_009552 2026-08-11 09:41:53 1
CONN
 
Resource Report
Resource Website
1000+ mentions
CONN (RRID:SCR_009550) CONN software application, software toolkit, image analysis software, software resource, data processing software Matlab based cross platform software package for computation, display, and analysis of functional connectivity in fMRI (fcMRI). Used for resting state data (rsfMRI) as well as task related designs. Covers pipeline from raw fMRI data to hypothesis testing. fmri functional connectivity, resting state data, seed-based correlations, ROI-to-ROI graph analyses, group ICA, masked ICA, generalized PPI, ALFF, ICC, GCOR, LCOR, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
works with: Eagle Atlas Compilation for Vestibular Research
PMID:22642651
PMID:21889994
Free, Available for download, Freely available nlx_155730 www.nitrc.org/projects/conn SCR_009550 CONN toolbox, CONN - functional connectivity toolbox, Connectivity Toolbox (CONN) 2026-08-11 09:41:52 1127
CBFBIRN
 
Resource Report
Resource Website
1+ mentions
CBFBIRN (RRID:SCR_009543) CBFBIRN service resource, data or information resource, storage service resource, data set, data repository THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017.

A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users.
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Cerebral Blood Flow Database and Analysis Pipeline
has parent organization: University of California at San Diego; California; USA
NIH PMID:24151465 THIS RESOURCE IS NO LONGER IN SERVICE nlx_155722 http://www.nitrc.org/projects/cbfbirn SCR_009543 Cerebral Blood Flow Biomedical Informatics Research Network 2026-08-11 09:41:52 3
ASA - Advanced Source Analysis
 
Resource Report
Resource Website
1+ mentions
ASA - Advanced Source Analysis (RRID:SCR_012867) ASA software application, image analysis software, image processing software, software resource, data processing software A highly flexible EEG/ERP and MEG analysis package with a variety of source reconstruction, signal analysis and MRI processing features. ASA combines functional brain imaging with the visualization and incorporation of morphological information obtained from MRI or CT. ASA is a highly interactive and flexible software tool that can be applied to neuro-physiological and clinical brain research. ASA gives a realistic impression of your experimental configuration together with topographical mapping of EEG and MEG and the results of your analysis. ASA is developed for and by people dedicated to brain research. The concept of flexibility and openness covers even most complex analysis demands. The ASA environment is particularly attractive for those that wish to develop their own methods in third party packages like Matlab and use ASA for pre-processing and visualization purposes. eeg, meg, electrocorticography, event related potential, fourier time-domain analysis, software, spectral analysis, temporal transformation, time domain analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Commercial license nlx_155691 http://www.nitrc.org/projects/asa SCR_012867 Advanced Source Analysis 2026-08-11 09:42:33 3
MeshView
 
Resource Report
Resource Website
10+ mentions
MeshView (RRID:SCR_017222) web service, software resource, data access protocol Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: LocaliZoom
is related to: Allen Institute for Brain Science
has parent organization: University of Oslo; Oslo; Norway
works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain
works with: Allen Mouse Brain Reference Atlas
works with: Waxholm Space
European Union Horizon 2020 Human brain project DOI:10.1371/journal.pone.0216796 Free, Freely available https://localiview.apps.ebrains.eu/, https://meshview-for-brain-atlases.readthedocs.io, https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases SCR_017222 MeshView for brain atlases 2026-08-11 09:43:40 11
vini: A viewer for fMRI data
 
Resource Report
Resource Website
vini: A viewer for fMRI data (RRID:SCR_017250) software application, data processing software, software resource, data visualization software Software Python tool as viewer for MRI data and numpy arrays. viewer, MRI, data, numpy, array is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Free, Available for download, Freely available https://github.com/lipsia-fmri/vini SCR_017250 2026-08-11 09:43:33 0
BrainSuite
 
Resource Report
Resource Website
50+ mentions
BrainSuite (RRID:SCR_006623) BrainSuite software application, image analysis software, software resource, data processing software, data visualization software Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Biomedical Informatics Research Network
NIBIB R01 EB002010;
NCRR P41 RR013642;
NIMH RO1-MH53213
PMID:12045000 nif-0000-30214 http://www.nitrc.org/projects/brainsuite SCR_006623 Brain Suite 2026-08-11 09:41:24 97
BrainVoyager Brain Tutor
 
Resource Report
Resource Website
1+ mentions
BrainVoyager Brain Tutor (RRID:SCR_006737) BV Brain Tutor software application, data or information resource, narrative resource, training material, software resource A free award-winning educational program that teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex. The program runs on Windows XP, Vista and Windows 7. atlas, brain, cerebral cortex, lobe of cerebral cortex, brodmann partition scheme region, functional area, human, magnetic resonance imaging assay, mri, 3d model, c++, macos, microsoft, magnetic resonance, software, win32 (ms windows), windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: BrainVoyager
has parent organization: Brain Innovation: Home of the BrainVoyager Product Family
Free nlx_144322 http://www.nitrc.org/projects/bvbraintutor, http://www.brainvoyager.com/BrainTutor.html SCR_006737 2026-08-11 09:41:25 3
BrainVoyager Brain Viewer
 
Resource Report
Resource Website
BrainVoyager Brain Viewer (RRID:SCR_006755) software application, data processing software, software resource, data visualization software Software that supports browsing and inspecting essential BrainVoyager data files as well as the header and content of DICOM files. The Viewer supports standard image files (JPEG, GIF, PNG, TIFF, BMP) allowing to inspect snapshots, figures or photos. Users can prepare a folder with selected data of a subject (VMRs, SRFs, Maps, snapshot images), which allows participants of fMRI measurements to browse their brain data and to show it to others. The Viewer can be handed over to colleagues not having a BrainVoyager license together with relevant data. This will allow them to view and explore your analyzed data files. dicom, brainvoyager, jpeg, gif, png, tiff, bmp, image, c++, ct, dicom, microsoft, magnetic resonance, pet, spect, visualization, win32 (ms windows), windows, windows xp is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Brain Innovation: Home of the BrainVoyager Product Family
Free, Available for download nlx_144321 http://www.nitrc.org/projects/bvviewer SCR_006755 BranVoyager, BV Brain Viewer 2026-08-11 09:41:27 0
NiftyReg
 
Resource Report
Resource Website
100+ mentions
NiftyReg (RRID:SCR_006593) NiftyReg software application, registration software, image analysis software, software resource, data processing software Software tools for global and local image registration. The algorithm used for global registration is based on a block matching approach enabling robust registration (outliers rejection). The local registration implementation uses a cubic B-Spline parametrisation (Free-Form Deformation). All registration algorithms are based on symmetric approaches where forward and backward transformations can be optimised concurrently. NiftyReg has been implemented for both CPU and GPU (through the use of CUDA). analyze, c, c++, nifti, nrrd, registration, resampling, spatial transformation, warping is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University College London; London; United Kingdom
BSD License nlx_155899 http://www.nitrc.org/projects/niftyreg SCR_006593 Nifty Reg 2026-08-11 09:41:25 246

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