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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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caGWAS Resource Report Resource Website |
caGWAS (RRID:SCR_009617) | caGWAS | software resource | Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data. | application, computational neuroscience, genetic association, genomic analysis, imaging genomics, java, snp, gene, software, web environment, microarray, genomic, immunohistochemistry, imaging, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Cancer Institute |
BSD License | nlx_155841 | http://www.nitrc.org/projects/cagwas | SCR_009617 | caGWAS (Cancer Genome-Wide Association Studies), Cancer Genome-Wide Association Studies, CGOM-caGWAS | 2026-09-19 12:51:50 | 0 | ||||||
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Slicer3 Module Rician noise filter Resource Report Resource Website 1+ mentions |
Slicer3 Module Rician noise filter (RRID:SCR_009614) | Slicer3:Module:Rician Noise Removal | data processing software, image processing software, software application, software resource | Two Slicer3 modules removing rician noise in diffusion tensor MRI | c++, console (text based), linux, magnetic resonance, posix/unix-like, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 3D Slicer |
NIH Roadmap for Medical Research ; NIBIB U54 EB005149; NCRR 2-P41-RR12553-07 |
PMID:17354881 | GNU General Public License | nlx_155836 | http://www.nitrc.org/projects/dtiricianrem | SCR_009614 | 2026-09-19 12:51:50 | 1 | |||||
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GIFTI Resource Report Resource Website 10+ mentions |
GIFTI (RRID:SCR_009579) | GIfTI | data or information resource, narrative resource, software resource, standard specification | Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI. | algorithm or reusable library, c, computational neuroscience, information resource, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroimaging Informatics Technology Initiative |
nlx_155761 | SCR_009579 | 2026-09-19 12:51:50 | 30 | |||||||||
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SVV Resource Report Resource Website |
SVV (RRID:SCR_009613) | SVV | data processing software, data visualization software, software application, software resource | Software application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results. | c, computed tomography, linux, magnetic resonance, nifti, pet, spect, posix/unix-like, rendering, software, surface rendering, visualization, neuroanatomy, surface, volume | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155835 | SCR_009613 | Surface and Volumetric Visualization | 2026-09-19 12:51:50 | 0 | |||||||
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NeuroWeb - NeuroImaging Database Resource Report Resource Website 1+ mentions |
NeuroWeb - NeuroImaging Database (RRID:SCR_009610) | NeuroWeb | software resource | Infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware. | computed tomography, magnetic resonance, pet, spect, mri, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155829 | http://www.nitrc.org/projects/neuroweb | SCR_009610 | 2026-09-19 12:51:50 | 1 | ||||||||
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Neuroimaging Made Easy Blog Resource Report Resource Website |
Neuroimaging Made Easy Blog (RRID:SCR_009611) | Neuroimaging Made Easy | blog, data or information resource, narrative resource, software resource | Blog presenting some scripts that can be used to facilitate and automate processing and analysis of brain data. In addition, it could be helpful explaining non clear stages and steps of brain data processing using some software such as; Freesurfer, FSL, Brainvoyager QX... At the moment, there are more than 10 applescripts in the main website http://www.easyneuroimaging.com that control different tools and commands (aparcstats2table, asegstats2table, BET, dcm2nii, FIRST, fslsplit, fslswapdim, fslview, mri_convert, Qdec, Recon-all, SIENAX, tkmedit, tksurfer) | analyze, applescript, application, ascii, dicom, linux, macos, mgh/mgz, magnetic resonance, nifti, posix/unix-like, sh/bash, unix shell, workflow, script | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Personal License | nlx_155830 | http://www.nitrc.org/projects/easy_neuroimage | SCR_009611 | 2026-09-19 12:51:50 | 0 | |||||||
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ERPLAB Resource Report Resource Website 100+ mentions |
ERPLAB (RRID:SCR_009574) | ERPLAB | data analysis software, data processing software, software application, software resource | A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH. | anova, eeg, meg, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Bioelectromagnetism Matlab Toolbox has parent organization: University of California at Davis; California; USA |
NIMH | GNU General Public License | nlx_155754 | http://www.nitrc.org/projects/erplab | SCR_009574 | ERPLAB Toolbox | 2026-09-19 12:51:50 | 463 | |||||
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EMSE Suite Resource Report Resource Website 10+ mentions |
EMSE Suite (RRID:SCR_009571) | EMSE Suite | data processing software, image analysis software, software application, software resource, software toolkit | A technically supported modular platform for space-time-frequency analyses of EEG/MEG/ECoG integrated (optionally) with structural MRI and functional hemodynamic measures (fMRI and NIRS). The Locator module uses Polhemus devices to acquire 3D sensor coordinates. Data Editor provides pipelines of spatial and temporal filters, and easy-to-use event pipelines for conditional binning of time, frequency, and time-frequency data across participants, with group results. Coherence, phase synchronication, and quasi-causal information assess connectivity. Source Estimator enables modeling of discrete overdetermined and distributed underdetermined sources, and spatial filtering for 3D brain regions of interest. Statistical nonparametric mapping (SnPM) may be performed for all measures. MR Viewer and Image Processor comprise tools for BEM and FEM volume conductor models, using cortical source space models. See http://www.sourcesignal.com/Features_EMSE_550.pdf for details and a supported free trial. | application, eeg, meg, electrocorticography, eeg modeling, forward - inverse, modeling, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155751 | http://www.nitrc.org/projects/emse | SCR_009571 | 2026-09-19 12:51:50 | 10 | |||||||
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LONI Brain Parser Resource Report Resource Website 1+ mentions |
LONI Brain Parser (RRID:SCR_009572) | Brain Parser | data processing software, image analysis software, segmentation software, software application, software resource | Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest. | analyze, anatomic, application, c++, console (text based), labeling, linux, microsoft, magnetic resonance, posix/unix-like, region of interest, segmentation, sh/bash, unix shell, windows, windows nt/2000, windows vista, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
GNU General Public License, LONI Software License | nlx_155783 | http://www.nitrc.org/projects/brainparser | SCR_009572 | BrainParser | 2026-09-19 12:51:50 | 3 | |||||
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MagVenture: MagPro Magnetic Stimulator Resource Report Resource Website 10+ mentions |
MagVenture: MagPro Magnetic Stimulator (RRID:SCR_009601) | MagPro | instrument resource | A complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry. | experiment control, hardware, magnetic resonance, response monitoring, stimulus presentation, clinical, neurophysiology, neurology, cognitive neuroscience, rehabilitation, psychiatry, instrument, equipment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is provided by: MagVenture |
Commercial license | nlx_155803 | http://www.nitrc.org/projects/magpro | SCR_009601 | MagPro Magnetic Stimulator (TMS) | 2026-09-19 12:51:50 | 10 | ||||||
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Mag Design and Engineering Resource Report Resource Website 1+ mentions |
Mag Design and Engineering (RRID:SCR_009600) | Mag Design & Engineering | commercial organization | A variety of MEG- and fMRI-compatible hardware for research use including typical response collection devices such as joysticks, response pads, mice, as well as stimulation devices such as vibrotactile stimulators, olfactometers, and pressure/force generators. The company also offers custom design and production services for many different applications. | mag, eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, optical imaging, physiological recording, response monitoring, stimulus presentation, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155802 | http://www.magconcept.com | SCR_009600 | 2026-09-19 12:51:50 | 6 | |||||||
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Distributome Resource Report Resource Website |
Distributome (RRID:SCR_009564) | Distributome | software resource | An open-source, open content-development project for exploring, discovering, navigating, learning, and computational utilization of diverse probability distributions. | computational neuroscience, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155746 | http://www.nitrc.org/projects/distributome | SCR_009564 | 2026-09-19 12:51:50 | 0 | |||||||
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DTIProcess ToolKit Resource Report Resource Website |
DTIProcess ToolKit (RRID:SCR_009561) | DTIProcess | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | A DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess, et al.. | c++, console (text based), macos, microsoft, modeling, magnetic resonance, nrrd, posix/unix-like, resampling, spatial transformation, tensor metric, tractography, windows, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of Utah; Utah; USA works with: NIAG Addiction Data |
BSD License | nlx_155741 | http://www.nitrc.org/projects/dtiprocess | SCR_009561 | 2026-09-19 12:51:50 | 0 | |||||||
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ProbabilisticBiasCorrection Resource Report Resource Website |
ProbabilisticBiasCorrection (RRID:SCR_009638) | ProbabilisticBiasCorrection | software resource | A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
3D Slicer License | nlx_155926 | SCR_009638 | 2026-09-19 12:51:51 | 0 | ||||||||
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Program for optimal design of blocked fMRI experiments Resource Report Resource Website |
Program for optimal design of blocked fMRI experiments (RRID:SCR_009639) | POBE | software resource | Computer program that provides a graphical user interface for fMRI researchers to easily and efficiently design their blocked experiments. The computer program POBE calculates the optimal number of subjects and the optimal scanning time for user specified experimental factors and model parameters so that the statistical efficiency is maximised for a given study budget. POBE can also be used to determine the minimum budget for a given power. Furthermore, a maximin design can be determined as efficient design for a possible range of values for the unknown model parameters. | magnetic resonance, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155927 | SCR_009639 | Program for optimal design of blocked experiments | 2026-09-19 12:51:51 | 0 | |||||||
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Rockland Download Link Script Resource Report Resource Website 1+ mentions |
Rockland Download Link Script (RRID:SCR_009513) | Rockland Download Link Script | software resource | Script which points browser to Nathan Kline Institute (NKI) Rockland Sample. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample |
Creative Commons License | nlx_155675 | SCR_009513 | 2026-09-19 12:51:49 | 1 | ||||||||
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Subject Order-Independent Group ICA Resource Report Resource Website 10+ mentions |
Subject Order-Independent Group ICA (RRID:SCR_009514) | SOI-GICA | software resource | While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage. | analyze, gnome, independent component analysis, kde, linux, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, software, statistical operation, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20338245 | GNU General Public License | nlx_155676 | SCR_009514 | 2026-09-19 12:51:49 | 18 | |||||||
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Pipeline Neuroimaging VirtualEnvironment Resource Report Resource Website |
Pipeline Neuroimaging VirtualEnvironment (RRID:SCR_009635) | PNVE | software resource | A self-contained virtual machine that can be executed on a common laptop or desktop, enabling the Pipeline to run virtually anywhere. Neophytes to the Pipeline can have their own private server running in minutes, software engineers and workflow designers can use the PNVE as a sandbox, and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment. | domain independent |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155923 | SCR_009635 | LONI Pipeline Neuroimaging Virtual Environment | 2026-09-19 12:51:50 | 0 | |||||||
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Network Modification Tool Lite Resource Report Resource Website |
Network Modification Tool Lite (RRID:SCR_009511) | NeMo Tool | software resource | Tool that associates localized white matter (WM) lesions with disruptions in gray matter connectivity as a step toward understanding the lesions? functional implications. A Tractogram Reference Set (TRS), i.e. collections of white matter fibers, is constructed from 73 normal healthy individuals and coregistered to a common space (MNI). The NeMo Tool uses the TRS to assess structural network disruption due to a particular WM lesion mask on a region and network-wise level. This tool is an easy way for researchers and clinicians to investigate changes in the structural brain network without having to perform tractography on their own normal data or on diseased/injured brains where the results may not represent the underlying physiology. | computational neuroscience | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155673 | SCR_009511 | Network Modification (NeMo) Tool Lite | 2026-09-19 12:51:49 | 0 | |||||||
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Non-rigid groupwise registration method Resource Report Resource Website |
Non-rigid groupwise registration method (RRID:SCR_009512) | Non-rigid groupwise registration method | data processing software, image analysis software, registration software, software application, software resource | An open source implementation of a non-rigid groupwise registration method. This project is implemented by Serdar K Balci (serdar at csail.mit.edu) and supervised by Polina Golland and William M. Wells All metrics are implementing in a multi-threaded fashion. The algorithm will run faster on computers with multiple CPU''s. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
nlx_155674 | SCR_009512 | 2026-09-19 12:51:49 | 0 |
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