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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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iTools Resource Report Resource Website 50+ mentions |
iTools (RRID:SCR_009626) | iTools | data access protocol, data or information resource, data repository, database, service resource, software repository, software resource, storage service resource, web service | 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 | 2026-09-05 06:26:35 | 53 | |||
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DFCI Biospecimen Repository Core Facility Resource Report Resource Website |
DFCI Biospecimen Repository Core Facility (RRID:SCR_009747) | access service resource, biospecimen repository, core facility, material storage repository, service resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core facility that provides the following services: Storage services for -80 degrees C and -190 degrees C in secure facility. The Biospecimen Repository provides long-term storage of clinical and research material in -80 degrees C and liquid nitrogen freezers located at Dana Farber''s Harbor Campus. Transportation of samples to and from Harbor Campus is provided by the facility for a small fee. Competitive prices are available on per box or per freezer basis in both segregated or non-segregated environments. |
material storage |
is listed by: Eagle I has parent organization: Dana-Farber Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156208 | http://research4.dfci.harvard.edu/issues/DryDock, http://www.dana-farber.org/Research/Core-Facilities.aspx#biospecimen | SCR_009747 | 2026-09-05 06:26:36 | 0 | ||||||||
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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, image processing software, software application, 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) |
Junta de Castilla y Leon ; Ministerio de Ciencia y Educacion |
Free, Available for download, Freely available | nlx_155649, SCR_014129 | SCR_009502 | Joint Anisotropic LMMSE Filter for Stationary Rici | 2026-09-05 06:26:33 | 1 | |||||||
|
fanDTasia Java Applet: DT-MRI Processing Resource Report Resource Website 1+ mentions |
fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) | fdt | data processing software, image processing software, software application, software resource | 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 | 2026-09-05 06:26:35 | 2 | |||||
|
JIP Analysis Toolkit Resource Report Resource Website 10+ mentions |
JIP Analysis Toolkit (RRID:SCR_009588) | JIP Toolkit | data processing software, image analysis software, software application, software resource, software toolkit | 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 | 2026-09-05 06:26:34 | 29 | |||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:26:35 | 937 | |||||
|
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 | 2026-09-05 06:26:33 | 0 | |||||||
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HAMMER Suite Resource Report Resource Website 1+ mentions |
HAMMER Suite (RRID:SCR_009583) | HAMMER Suite | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | 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 | 2026-09-05 06:26:34 | 1 | ||||||
|
eConnectome Resource Report Resource Website 10+ mentions |
eConnectome (RRID:SCR_009618) | eConnectome | data processing software, image analysis software, image processing software, software application, software resource | 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 | 2026-09-05 06:26:35 | 31 | |||||
|
Brainsight Resource Report Resource Website 50+ mentions |
Brainsight (RRID:SCR_009539) | Brainsight | resource, software 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 | 2026-09-05 06:26:34 | 68 | |||||||
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BrainMagix SPM Viewer Resource Report Resource Website 1+ mentions |
BrainMagix SPM Viewer (RRID:SCR_009537) | BrainMagix SPM Viewer | data processing software, data visualization software, software application, software resource | 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 | 2026-09-05 06:26:34 | 1 | |||||||
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SCALCE Resource Report Resource Website |
SCALCE (RRID:SCR_009658) | SCALCE | software resource | A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00969 | SCR_009658 | Boosting Sequence Compression Algorithms using Locally Consistent Encoding | 2026-09-05 06:26:36 | 0 | |||||||||
|
Generic Exome Analysis Plan Resource Report Resource Website |
Generic Exome Analysis Plan (RRID:SCR_009656) | data or information resource, experimental protocol, narrative resource | Outline of a generic plan for analysis of a whole exome sequencing project. |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
nlx_156093 | SCR_009656 | 2026-09-05 06:26:36 | 0 | |||||||||||
|
BSMac Resource Report Resource Website |
BSMac (RRID:SCR_009531) | BSMac | data processing software, image analysis software, software application, software resource, software toolkit | 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 | 2026-09-05 06:26:34 | 0 | |||||
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SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-09-05 06:26:36 | 21 | |||||||
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GTRACT Resource Report Resource Website 1+ mentions |
GTRACT (RRID:SCR_009651) | GTRACT | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | 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 | 2026-09-05 06:26:36 | 2 | ||||
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DATAPixx Resource Report Resource Website 10+ mentions |
DATAPixx (RRID:SCR_009648) | DATAPixx | commercial organization | Supplies a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision. | eeg, eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, physiological recording, response monitoring, stimulus presentation, vision | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155989 | http://www.nitrc.org/projects/vpixx | SCR_009648 | 2026-09-05 06:26:35 | 15 | |||||||
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REST: a toolkit for resting-state fMRI Resource Report Resource Website 1000+ mentions |
REST: a toolkit for resting-state fMRI (RRID:SCR_009641) | REST | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files. | correlation, cross-correlation, fourier time-domain analysis, gnome, kde, linux, macos, matlab, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, two dimensional display, visualization, windows, resting-state functional magnetic resonance imaging, resting-state fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National High Technology Program of China ; National Natural Science Foundation of China ; Program for Changjiang Scholars and Innovative Research Team in University |
PMID:21949842 | Academic Free License | nlx_155936 | http://www.nitrc.org/projects/rest | SCR_009641 | Resting-State fMRI Data Analysis Toolkit, REsting State fMRI Data analysis Toolkit | 2026-09-05 06:26:35 | 1004 | ||||
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Robust Biological Parametric Mapping Resource Report Resource Website 1+ mentions |
Robust Biological Parametric Mapping (RRID:SCR_009642) | Robust Biological Parametric Mapping | software resource | To enable widespread application of the Biological parametric mapping (BPM) approach, they introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model. Biological parametric mapping (BPM) has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects. | magnetic resonance, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155944 | SCR_009642 | 2026-09-05 06:26:35 | 3 | ||||||||
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QCQP Resource Report Resource Website |
QCQP (RRID:SCR_009640) | QCQP | data processing software, image analysis software, image processing software, segmentation software, software application, software resource | Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction. | magnetic resonance, classification, segmentation, bias field correction | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155932 | SCR_009640 | Quadratically constrained quadratic programing | 2026-09-05 06:26:35 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
