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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Multi-fiber Reconstruction from DW-MRI Resource Report Resource Website |
Multi-fiber Reconstruction from DW-MRI (RRID:SCR_009509) | Multi-fiber Reconstruction from DW-MRI | software resource | This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program, namely, Mixture of Wisharts (MOW), Diffusion Orientation Transform (DOT) and Q-ball Imaging (QBI). This program is mainly developed and maintained by Bing Jian, as part of his Ph.D. research, supervised by Prof. Baba Vemuri. Please note that the source code of this program is hosted at Google Code, see the Source Code link on the left. | reusable library, console (text based), diffusion mr fiber tracking, fiber tracking, magnetic resonance, os independent, python, tractography, reconstruction, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
GNU General Public License | nlx_155669 | SCR_009509 | 2026-02-14 02:01:50 | 0 | ||||||||
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MASIMatlab Resource Report Resource Website 1+ mentions |
MASIMatlab (RRID:SCR_009506) | MASIMatlab | software resource | This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling. | magnetic resonance, matlab, population characterization, mri, dti, smri, qmri, shape modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
nlx_155655 | SCR_009506 | 2026-02-14 02:01:50 | 4 | |||||||||
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iView X MRI-LR - Eye Tracking for fMRI Resource Report Resource Website 1+ mentions |
iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) | iView X MRI-LR | software resource | A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output | magnetic resonance, fmri, meg, eye, eye tracking, mri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commerical | nlx_155853 | http://www.nitrc.org/projects/iviewx_mri-lr | SCR_009627 | 2026-02-14 02:01:53 | 3 | |||||||
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MASI Label Fusion Resource Report Resource Website 1+ mentions |
MASI Label Fusion (RRID:SCR_009505) | MASI Label Fusion | software resource | Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
GNU Lesser General Public License | nlx_155654 | SCR_009505 | 2026-02-14 02:01:40 | 3 | ||||||||
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iTools Resource Report Resource Website 10+ mentions |
iTools (RRID:SCR_009626) | iTools | data repository, storage service resource, web service, software repository, data or information resource, service resource, data access protocol, software resource, database | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools http://www.loni.usc.edu/research/software |
http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-02-14 02:01:52 | 45 | |||
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Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI Resource Report Resource Website 1+ mentions |
Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI (RRID:SCR_009502) | data processing software, software application, image processing software, software resource, standalone software | This module reduces Rician noise on nhdr/nrrd DWIs. Filters image in mean squared error sense using Rician noise model. All estimations are performed as sample estimates in a "shaped neighborhood" defined by the weights extracted from structural similarity of voxels following same idea as in Non-Local Means filter. | reduce Rician noise, Rician noise model, image filter, |
uses: Insight Segmentation and Registration Toolkit is used by: 3D Slicer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Ministerio de Ciencia y Educacion ; Junta de Castilla y Leon |
Free, Available for download, Freely available | nlx_155649, SCR_014129 | SCR_009502 | Joint Anisotropic LMMSE Filter for Stationary Rici | 2026-02-14 02:01:50 | 1 | |||||||
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fanDTasia Java Applet: DT-MRI Processing Resource Report Resource Website 1+ mentions |
fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) | fdt | image processing software, software resource, data processing software, software application | A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser. | magnetic resonance, dti, diffusion-weighted mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NIBIB EB007082; NINDS NS066340 |
Non-Commercial Software License Agreement, Https://www.nitrc.org/include/glossary.php#589, Non-commercial | nlx_155849 | http://www.nitrc.org/projects/fandtasia | SCR_009624 | FanDTasia | 2026-02-14 02:01:52 | 2 | |||||
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JIP Analysis Toolkit Resource Report Resource Website 10+ mentions |
JIP Analysis Toolkit (RRID:SCR_009588) | JIP Toolkit | data processing software, software toolkit, software application, software resource, image analysis software | Software toolkit for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for fMRI time series analysis, a 1st-order GLM analysis for PET data within the SRTM framework, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 4) MRI templates to place your rodent and non-human primate data into standardized spaces. | affine warp, atlas application, atlas data, c, console (text based), image display, image-to-image, linux, macos, magnetic resonance, nifti, nonlinear warp, pet, spect, posix/unix-like, registration, resampling, spatial transformation, time domain analysis, visualization, warping, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard Medical School; Massachusetts; USA |
NIBIB R03EB008134 | MGH CSRL License | nlx_155778 | http://www.nitrc.org/projects/jip | SCR_009588 | JIP fMRI Analysis Toolkit | 2026-02-14 02:01:52 | 21 | |||||
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MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, software resource, data processing software, software application | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach https://bio.tools/mach |
https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-02-14 02:01:53 | 925 | |||||
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BRAINSROIAuto Resource Report Resource Website |
BRAINSROIAuto (RRID:SCR_009501) | BRAINSROIAuto | software resource | Automatically creates a mask based on the "foreground" of an anatomical scan volume. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
BRAINS License | nlx_155703 | http://www.nitrc.org/projects/brainsroiauto | SCR_009501 | 2026-02-14 02:01:40 | 0 | |||||||
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HAMMER Suite Resource Report Resource Website 1+ mentions |
HAMMER Suite (RRID:SCR_009583) | HAMMER Suite | data processing software, software toolkit, software application, image processing software, software resource, image analysis software | The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration. | magnetic resonance, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:12575879 | Free | nlx_155769 | http://www.nitrc.org/projects/hammer_suite | SCR_009583 | 2026-02-14 02:01:41 | 1 | ||||||
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eConnectome Resource Report Resource Website 10+ mentions |
eConnectome (RRID:SCR_009618) | eConnectome | data processing software, software application, image processing software, software resource, image analysis software | An open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome La Sapienza. | eeg, meg, electrocorticography, forward - inverse, matlab, microsoft, modeling, multivariate analysis, region of interest, segmentation, statistical operation, visualization, windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIBIB RO1 EB006433; NIBIB RO1 EB007920 |
GNU General Public License | nlx_155844 | http://www.nitrc.org/projects/econnectome | SCR_009618 | Electrophysiological Connectome | 2026-02-14 02:01:52 | 30 | |||||
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Brainsight Resource Report Resource Website 50+ mentions |
Brainsight (RRID:SCR_009539) | Brainsight | software resource, resource | Neuronavigation system for use in human cognitive neuroscience (TMS, EEG, NIRS) and for non-human neurosurgical applications. | dicom, eeg, eeg, meg, electrocorticography, hardware, minc, minc2, magnetic resonance, nifti, nirs/fnir, optical imaging, optical imaging, philips par/rec, physiological recording, rendering, surface rendering, visualization, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Comercial Licence | nlx_155718 | http://www.nitrc.org/projects/brainsight | SCR_009539 | 2026-02-14 02:01:51 | 62 | |||||||
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BrainMagix SPM Viewer Resource Report Resource Website 1+ mentions |
BrainMagix SPM Viewer (RRID:SCR_009537) | BrainMagix SPM Viewer | data visualization software, software resource, data processing software, software application | A free, professional viewer for SPM fMRI results. SPM (Statistical Parametric Mapping, UCL, London) is a powerful fMRI analysis software but its visualization capabilities are sometimes a limitation for the researchers. That's why Imagilys has decided to offer the neuroimaging community a free version of its commercial "BrainMagix" neuroimaging software, called "BrainMagix SPM viewer". BrainMagix SPM Viewer's Features - Professional viewer for your SPM-based fMRI activations - JAVA-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed - Reads SPM.mat files and NIfTI images in an user-friendly way - Overlay the blobs with an atlas or any anatomical image - On the fly adjustment of threshold and cluster size - Localize your activations in an atlas - BOLD signal curves in ROIs (future feature) - Export your results as PNG images | java, magnetic resonance, nifti, os independent, visualization, statistical parametric mapping, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM |
Other/Commercial license License, Free | nlx_155714 | http://www.nitrc.org/projects/bm_spm_viewer | SCR_009537 | 2026-02-14 02:01:52 | 1 | |||||||
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BSMac Resource Report Resource Website |
BSMac (RRID:SCR_009531) | BSMac | data processing software, software toolkit, software application, software resource, image analysis software | A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results. | computational neuroscience, magnetic resonance, brain activation, connectivity, matlab, statistics, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Emory University; Georgia; USA |
PMID:22101143 PMID:17936016 |
Acknowledgement requested, BSD License, GNU Lesser General Public License, GNU General Public License | nlx_155706 | http://www.nitrc.org/projects/bsmac | SCR_009531 | BSMAC Software, Bayesian Spatial Model for Brain Activation and Connectivity, BSMac: Bayesian Spatial Model for Brain Activation and Connectivity | 2026-02-14 02:01:41 | 0 | |||||
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JHU Proj. in Applied Medical Imaging Resource Report Resource Website |
JHU Proj. in Applied Medical Imaging (RRID:SCR_009499) | JHU Proj. in Applied Medical Imaging | software resource | This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
Free | nlx_155647 | SCR_009499 | 2026-02-14 02:01:50 | 0 | ||||||||
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INCF Neuroimaging Data Sharing Resource Report Resource Website |
INCF Neuroimaging Data Sharing (RRID:SCR_009497) | INCF Neuroimaging Data Sharing | data or information resource, narrative resource, standard specification | Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications. | community, knowledge environment, loni pipeline, magnetic resonance, nipype |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: International Neuroinformatics Coordinating Facility |
Creative Commons License | nlx_155645 | SCR_009497 | 2026-02-14 02:01:50 | 0 | ||||||||
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GTRACT Resource Report Resource Website 1+ mentions |
GTRACT (RRID:SCR_009651) | GTRACT | data processing software, software toolkit, software application, image processing software, software resource, image analysis software | A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools | c++, dicom, macos, microsoft, modeling, morphology, magnetic resonance, nifti, posix/unix-like, quantification, tensor metric, tractography, windows, dti, diffusion tensor fiber tracking, fiber tracking, nrrd, algorithm, connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of Iowa; Iowa; USA |
Aging | NARSAD ; NINDS R01NS050568-01A2S1; NINDS 5R01NS040068-04; NIMH 5R01MH063405-04; NIMH 5R01MH031593-23; NIMH 2R01MH040856-17A2; NIA 5K23AG020649-03; NIDCR 5R01DE014399-04 |
PMID:16631385 | BSD License | nlx_155992 | SCR_009651 | Guided Tensor Restore Anatomical Connectivity Tractography | 2026-02-14 02:01:42 | 2 | ||||
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IDeA Lab brain image processing suite Resource Report Resource Website 1+ mentions |
IDeA Lab brain image processing suite (RRID:SCR_009495) | IDeA Lab brain image processing suite | data processing software, software toolkit, software application, software resource, image analysis software | Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added. | analyze, c++, console (text based), csh/tcsh, image display, image-to-image, image-to-template, intermodal, intersubject, linux, magnetic resonance, nifti, nonlinear warp, posix/unix-like, quantification, registration, resampling, spatial transformation, spline interpolation, tri-linear, two dimensional display, unix shell, visualization, volume measurement, volumetric analysis, warping | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155644 | SCR_009495 | 2026-02-14 02:01:51 | 1 | |||||||||
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Groupwise Image Registration Toolbox Resource Report Resource Website |
Groupwise Image Registration Toolbox (RRID:SCR_009492) | Groupwise Image Registration | data processing software, software application, registration software, software resource, image analysis software | A method for group-wise image registration by pairwisely registering similar images identified using graph theoretic techniques. Particularly, they use sparse coding to estimate image similarity measures among images to be registered, yielding asymmetric, group-wise image similarity measures for each image to others in the group. | domain independent |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
PAMI License, Http://www.nitrc.org/include/glossary.php#690, Non-commercial | nlx_155640 | SCR_009492 | 2026-02-14 02:01:50 | 0 |
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