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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | |||||||
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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 | ||||||
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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 | ||||||||
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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 | |||||||
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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 | |||||||
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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 | ||||||
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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 | ||||||||
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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 | ||||||||
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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 | ||||||
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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 | ||||||
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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 | ||||||
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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 | |||||
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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 | ||||
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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 | ||||||
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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 | ||||||
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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 | |||||||||
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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 | |||||
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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 | |||||||
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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 | |||||||
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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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