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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ODIN Resource Report Resource Website 10+ mentions |
ODIN (RRID:SCR_001386) | ODIN | software resource, source code, service resource | Service (Beta) that allows users to search the DataCite Metadata Store, and add their research outputs including datasets, software, and others to their ORCID profile. This should increase the visibility of these research data, and will make it easier to use these data citations in applications that connect to the ORCID Registry. In addition, the service is also providing formatted citations in several popular citation styles, supports COinS, links to related resources, and displays the attached Creative Commons license where this information is available. The DataCite Metadata Store of course also contains many text documents from academic publishers and services such as figshare or PeerJ Preprints, and these works can also be claimed. This tool is a collaborative effort by ORCID, CrossRef and DataCite. | data citation, scholarly communication, interoperability, access, discovery, sustainability, digital object identifier |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ORCID - Open Researcher and Contributor ID has parent organization: DataCite |
European Union FP7 Coordination and Support Action 312788 | Unless otherwise noted, Creative Commons Attribution License, Account required | nlx_152557 | http://www.nitrc.org/projects/od1n http://github.com/mfenner/cr-search | SCR_001386 | ORCID and DataCite Interoperability Network | 2026-02-14 02:06:01 | 28 | |||||
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NINDS Repository Resource Report Resource Website 1+ mentions |
NINDS Repository (RRID:SCR_004520) | biomaterial supply resource, material resource | Open resource of biological samples (DNA, cell lines, and other biospecimens) and corresponding phenotypic data to promote neurological research. Samples from more than 34,000 unique individuals with cerebrovascular disease, dystonia, epilepsy, Huntington's Disease, motor neuron disease, Parkinsonism, and Tourette Syndrome, as well as controls (population control and unaffected relatives) have been collected. The mission of the NINDS Repository is to provide 1) genetics support for scientists investigating pathogenesis in the central and peripheral nervous systems through submissions and distribution; 2) information support for patients, families, and advocates concerned with the living-side of neurological disease and stroke. | nervous system disorder, neurogenetics, genetic, clinical data, cerebrovascular disease, epilepsy, motor neuron disease, parkinson's disease, parkinsonism, tourette's disorder, normal control, stroke, amyotrophic lateral sclerosis, huntington's disease, dystonia, dementia, neurologically normal, blood, dna, biomarker, plasma, urine, cell line, induced pluripotent stem cell, fibroblast, stem cell, frozen, lymphoblast, biospecimen banking, biospecimen processing, biospecimen distribution, biospecimen, genetics, phenotype, neurological disease |
is listed by: One Mind Biospecimen Bank Listing is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PD-DOC is related to: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) has parent organization: Coriell Cell Repositories |
Cerebrovascular disease, Epilepsy, Motor neuron disease, Parkinson's disease, Tourette's Disorder, Normal control, Stroke, Amyotrophic Lateral Sclerosis, Huntington's disease, Dystonia, Dementia, Neurologically normal, Neurological disorder | NINDS ; NIH Blueprint for Neuroscience Research |
Public | nlx_143800 | SCR_004520 | NINDS Human Genetics DNA Cell Line Repository, NINDS Human Genetics DNA and Cell Line Repository, The NINDS Repository, The NINDS Human Genetics Resource Center, The NINDS Human Genetics DNA and Cell Line Repository | 2026-02-14 02:06:47 | 3 | ||||||
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Brain Connectivity Toolbox Resource Report Resource Website 100+ mentions |
Brain Connectivity Toolbox (RRID:SCR_004841) | BCT | software resource, software toolkit | A large selection of complex network measures in Matlab that are increasingly used to characterize structural and functional brain connectivity datasets. Several people have contributed to the toolbox, and if you wish to contribute with a new function or set of functions, please contact Olaf Sporns. All efforts have been made to avoid errors, but users are strongly urged to independently verify the accuracy and suitability of toolbox functions for the chosen application. Please report bugs or substantial improvements. | brain, connectivity, matlab, brain network, c++, structure, function, brain connectivity, matlab, magnetic resonance, os independent, statistical operation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Connectome Coordination Facility is related to: Graphtools has parent organization: Indiana University; Indiana; USA |
CSIRO ICT Centre scholarship ; J.S. McDonnell Foundation Brain NRG JSMF22002082 |
PMID:19819337 | nlx_143925 | http://www.nitrc.org/projects/bct | SCR_004841 | 2026-02-14 02:07:06 | 324 | ||||||
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Object-Oriented Development Interface for NMR Resource Report Resource Website 10+ mentions |
Object-Oriented Development Interface for NMR (RRID:SCR_005974) | ODIN | software resource, software application | A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms. | analyze, c++, console (text based), dicom, image display, image reconstruction, modeling, magnetic resonance, nifti, os independent, simulation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: SourceForge |
GNU General Public License | nlx_155909 | https://sources.debian.org/src/odin/ | SCR_005974 | Object Oriented Development Interface for NMR, ODIN - Object-Oriented Development Interface for NMR | 2026-02-14 02:06:39 | 15 | ||||||
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DONE: Detection of Outlier NEurons Resource Report Resource Website |
DONE: Detection of Outlier NEurons (RRID:SCR_005299) | DONE | software resource, software application | Software that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface. | neuron, feature-space, archetype, outlier, matlab, neuromorphometry, computational neuroscience |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NeuroMorpho.Org has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
FAPESP 05/00587-5; CNPq 301303/06-1; CNPq 573583/2008-0; FAPESP sponsorship 2010/01994-1; FAPESP sponsorship 2010/16310-0; EPSRC EP/G03950X/1; EPSRC EP/E002331/1; National Research Foundation of Korea R32-10142 |
PMID:22615032 | GNU General Public License | nlx_144348 | http://www.nitrc.org/projects/done | SCR_005299 | Detection of Outlier NEurons | 2026-02-14 02:06:37 | 0 | ||||
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Mesh-based Monte Carlo (MMC) Resource Report Resource Website |
Mesh-based Monte Carlo (MMC) (RRID:SCR_006950) | MMC | software resource, software application | A Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores. | c, console (text based), modeling, monte carlo, optical imaging, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155810 | http://www.nitrc.org/projects/mmc | SCR_006950 | Mesh-based Monte Carlo | 2026-02-14 02:06:40 | 0 | ||||||
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NODDI Matlab Toolbox Resource Report Resource Website 10+ mentions |
NODDI Matlab Toolbox (RRID:SCR_006826) | NODDI Matlab Toolbox | software resource, software toolkit | This MATLAB toolbox implements a data fitting routine for Neurite Orientation Dispersion and Density Imaging (NODDI). NODDI is a new diffusion MRI technique for imaging brain tissue microstructure. Compared to DTI, it has the advantage of providing measures of tissue microstructure that are much more direct and hence more specific. It achieves this by adopting the model-based strategy which relates the signals from diffusion MRI to geometric models of tissue microstructure. In contrast to typical model-based techniques, NODDI is much more clinically feasible and can be acquired on standard MR scanners with an imaging time comparable to DTI. | analyze, matlab, magnetic resonance, nifti, os independent, neurite orientation dispersion and density imaging, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Artistic License | nlx_155892 | http://www.nitrc.org/projects/noddi_toolbox | SCR_006826 | 2026-02-14 02:07:03 | 25 | |||||||
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dinifti Resource Report Resource Website 1+ mentions |
dinifti (RRID:SCR_000303) | dinifti | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format. | analyze, console (text based), dicom, format conversion, freebsd, linux, magnetic resonance, nifti, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: New York University; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155843 | http://www.nitrc.org/projects/dinifti http://cbi.nyu.edu/software/dinifti.php https://sources.debian.org/src/dicomnifti/ |
SCR_000303 | NYU CBI DICOM to NIfTI Converter | 2026-02-14 02:06:28 | 2 | ||||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. | c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155961 | http://www.nitrc.org/projects/shapeworks | SCR_000424 | 2026-02-14 02:06:58 | 1 | ||||||
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CIFTI Connectivity File Format Resource Report Resource Website 1+ mentions |
CIFTI Connectivity File Format (RRID:SCR_000852) | CIFTI Connectivity File Format | systems interoperability software, software resource, software application | Standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties. Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats. Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155527 | SCR_000852 | Connectivity Informatics Technology Initiative Connectivity File Format | 2026-02-14 02:06:59 | 7 | |||||||
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Group Level Imputation of Statistic Maps Resource Report Resource Website |
Group Level Imputation of Statistic Maps (RRID:SCR_002397) | Group Level Imputation of Statistic Maps | software resource, software toolkit | A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R). | magnetic resonance, imputation, t-test, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155768 | SCR_002397 | 2026-02-14 02:07:01 | 0 | ||||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software resource, software toolkit, software application | A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished. | reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: neurodebian |
Free, Available for download, Freely available | nlx_155536 | http://www.nitrc.org/projects/cmtk https://sources.debian.org/src/cmtk/ |
SCR_002234 | Computational Morphometry Toolkit (CMTK) | 2026-02-14 02:07:01 | 33 | ||||||
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RFT FDR Resource Report Resource Website |
RFT FDR (RRID:SCR_002533) | RFT_FDR | software resource, software application | So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171). | console (text based), gnome, kde, matlab, mgh/mgz, modeling, magnetic resonance, os independent, rendering, statistical operation, surface analysis, surface rendering, thickness, visualization, random field theory |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155938 | SCR_002533 | RFT-FDR, RFT FDR | 2026-02-14 02:07:01 | 0 | |||||||
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NIRx2nirs: A NIRx to .nirs data converter Resource Report Resource Website 1+ mentions |
NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) | NIRx2nirs | software resource, software application | A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge. | hardware, nirs, fnir, optical imaging, optical imaging, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Homer2 |
Free, Available for download, Freely available | nlx_155887 | SCR_002492 | 2026-02-14 02:06:55 | 1 | ||||||||
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Stereo Investigator Resource Report Resource Website 100+ mentions |
Stereo Investigator (RRID:SCR_002526) | software resource, instrument resource | Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. | stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
Restricted | SciRes_000114, SCR_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | Stereo Investigator system | 2026-02-14 02:06:42 | 145 | |||||||
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Slicer3 Example Modules Resource Report Resource Website |
Slicer3 Example Modules (RRID:SCR_002559) | Slicer3 Example Modules | software resource, software application, software development tool | Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions | analyze, c++, console (text based), computed tomography, dicom, linux, macos, microsoft, magnetic resonance, nifti, pet, spect, platform or development environment, posix/unix-like, win32 (ms windows), windows, windows nt/2000, windows vista |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center |
Free, Available for download, Freely available | nlx_155965 | SCR_002559 | 2026-02-14 02:06:33 | 0 | ||||||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software resource, software toolkit, software application | A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics. | analyze, c, matlab, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows, parametric surface model, spherical harmonics, 3d, shape modeling, analysis, morphometry |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University School of Medicine; Indiana; USA |
NIBIB R03EB008674-01 | Free, Available for download, Freely available | nlx_155952 | http://www.nitrc.org/projects/spharm-mat | SCR_002545 | 2026-02-14 02:06:55 | 2 | ||||||
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Measure Projection Toolbox Resource Report Resource Website 1+ mentions |
Measure Projection Toolbox (RRID:SCR_002429) | MPT | software resource, software toolkit | This toolbox is an EEGLAB plugin for performing Measure Projection Analysis. Measure Projection Analysis (MPA) is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component (IC) clustering issues by abandoning the notion of distinct IC clusters. Instead, it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects and/or sessions as quantified by the values of various EEG measures. Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences. | reusable library, eeg, meg, electrocorticography, matlab, statistical operation, surrogate data analysis, visualization, measure projection analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Swartz Center for Computational Neuroscience |
Free, Available for download, Freely available | nlx_155809 | http://www.nitrc.org/projects/measure_project | SCR_002429 | Measure Projection Toolbox (MPT) | 2026-02-14 02:06:42 | 3 | ||||||
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cortex Resource Report Resource Website 100+ mentions |
cortex (RRID:SCR_002467) | cortex | software resource, software application | Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clinical neuroinformatics, mgh/mgz, magnetic resonance, r, surface analysis, thickness, mri, cortical thickness, morphometry, neuroimaging, power analysis, study design, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: bio.tools is listed by: Debian has parent organization: Brain Research Institute |
PMID:22807270 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155842, biotools:cortex | http://brain.org.au/software/cortex/power http://www.nitrc.org/projects/cortex https://bio.tools/cortex |
SCR_002467 | Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies | 2026-02-14 02:06:42 | 374 | |||||
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Diffusion Tractography with Kalman Filter Resource Report Resource Website |
Diffusion Tractography with Kalman Filter (RRID:SCR_002585) | Diffusion Tractography with Kalman Filter | software resource, software application | Software framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation. The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application. | c++, diffusion mr fiber tracking, fiber tracking, microsoft, magnetic resonance, nrrd, posix/unix-like, tractography, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:19694258 | Free, Available for download, Freely available | nlx_155990 | SCR_002585 | Tractography with Unscented Kalman Filter | 2026-02-14 02:06:42 | 0 |
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