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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BrainMagix SPM Viewer Resource Report Resource Website 1+ mentions |
BrainMagix SPM Viewer (RRID:SCR_009537) | BrainMagix SPM Viewer | software resource, software application, data visualization software, data processing software | 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 | 2026-08-08 11:59:13 | 1 | |||||||
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iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-08-08 11:59:21 | 11 | ||||||
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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 | 2026-08-08 11:59:24 | 21 | |||||||
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GTRACT Resource Report Resource Website 1+ mentions |
GTRACT (RRID:SCR_009651) | GTRACT | software toolkit, image processing software, image analysis software, software resource, software application, data processing 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 | 2026-08-08 11:59:26 | 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 | software toolkit, image analysis software, software resource, software application, data processing 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 | 2026-08-08 11:59:13 | 1 | |||||||||
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HD Neuro-Informatics Resource Report Resource Website 1+ mentions |
HD Neuro-Informatics (RRID:SCR_009493) | HDNI | data or information resource, portal, topical portal | An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Huntington''s disease | BSD License | nlx_155641 | SCR_009493 | Huntington Disease Nueroimaging Initiative | 2026-08-08 11:59:24 | 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 | 2026-08-08 11:59:15 | 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 | image processing software, software toolkit, image analysis software, software resource, software application, data processing software | 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 | 2026-08-08 11:59:15 | 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 | 2026-08-08 11:59:23 | 3 | ||||||||
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INVIZIAN Resource Report Resource Website 1+ mentions |
INVIZIAN (RRID:SCR_009549) | INVIZIAN | software resource, software application, data visualization software, data processing software | A visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once ?bringing together brain image data from some of the world?s best neuroscience research teams. INVIZIAN empowers both researchers and students of neuroscience to explore and understand the human brain using a simple yet powerful user interface for neuroimaging data exploration and discovery. See a beautiful example of a cloud of individual brains tumbling around in the INVIZIAN interface in Vimeo (http://vimeo.com/67984681). Visit often to see how we are making continuing progress to make Invizian even more amazing. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
LONI Software License | nlx_155775 | http://www.nitrc.org/projects/invizian | SCR_009549 | Informatics Visualization in Neuroimaging | 2026-08-08 11:59:22 | 1 | ||||||
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Oregon Health and Science University; Oregon; USA Resource Report Resource Website 1+ mentions |
Oregon Health and Science University; Oregon; USA (RRID:SCR_009665) | OHSU | university | As the state''s only health and research university, OHSU brings together patient care, research, education of the next generation of health care providers and scientists and community service to improve the health and well-being of all Oregonians. |
is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is parent organization of: OHSU MRI Support Core Laboratory is parent organization of: MCML and CONV is parent organization of: Neuron Registry Annotated Corpus is parent organization of: OHSU Biolibrary is parent organization of: Sterol and Isoprenoid Research Consortium is parent organization of: CTSAconnect is parent organization of: CTSA ShareCenter is parent organization of: OHSU Layton Aging and Alzheimer's Disease Center is parent organization of: Clinical Outcomes Research Initiative is parent organization of: OHSU Investigator Support and Integration Services is parent organization of: OHSU Advanced Computing Center Core Facility is parent organization of: OHSU Advanced Imaging Research Center Core Facility is parent organization of: OHSU Advanced Light Microscopy Core Facility is parent organization of: OHSU Assisted Reproductive Technologies and Embryonic Stem Cell Laboratory is parent organization of: OHSU Bioanalytical Shared Resource Pharmacokinetics Core Facility is parent organization of: OHSU Biochemical Genetics Laboratory is parent organization of: Oregon Clinical and Translational Research Institute Biomedical Informatics Program is parent organization of: OHSU Biomedical Informatics Shared Resource is parent organization of: OHSU Clinical Cytogenetics Laboratory is parent organization of: OHSU DNA Services Core Facility is parent organization of: Oregon Health and Science University Multiscale Microscopy Core Facility is parent organization of: OHSU Electronics and Instrumentation Design Core Resource is parent organization of: OHSU Endocrine Technology Support Core Laboratory is parent organization of: OHSU Flow Cytometry and Monoclonal Antibody Shared Resource Core Facility is parent organization of: OHSU Gene Profiling Shared Resource Core Facility is parent organization of: OHSU Lipid-Atherosclerosis Laboratory is parent organization of: OHSU Histopathology Shared Resource Core Facility is parent organization of: OHSU Imaging and Morphology Support Core Laboratory is parent organization of: OHSU Immuno Electron Microscopy Core is parent organization of: OHSU Immunology Support Core Cellular Immunology Unit is parent organization of: OHSU Immunology Support Core Flow Cytometry Unit is parent organization of: OHSU In Vivo Optical Imaging Center is parent organization of: OHSU Massively Parallel Sequencing Shared Resource Core Facility is parent organization of: OHSU Methamphetamine Abuse Research Center Animal Core Component is parent organization of: OHSU Molecular and Cellular Biology Core Laboratory is parent organization of: OHSU Monoclonal Antibody Core Laboratory is parent organization of: OHSU Neuropathology Core is parent organization of: OHSU Nuclear Magnetic Resonance Core Facility is parent organization of: OHSU Proteomics Shared Resource Core Facility is parent organization of: OHSU Research Cytogenetics Core Laboratory is parent organization of: OHSU Animal Model Support Core Facility is parent organization of: Oregon Clinical and Translational Research Institute Bionutrition Unit is parent organization of: OHSU Oregon Clinical and Translational Research Center Core Facility is parent organization of: Oregon Stem Cell Center Monoclonal Antibody Core is parent organization of: OSHU Gene Microarray Shared Resource is parent organization of: Oregon Health and Science University Labs and Facilities is parent organization of: OHSU DNA Services Core Facility is parent organization of: OHSU Molecular Virology Support Core is parent organization of: Oregon Health and Science University School of Medicine; Oregon; USA is parent organization of: Zebra Finch Expression Brain Atlas is parent organization of: Oregon Brain Bank is parent organization of: Research Network in Early Experience and Brain Development is parent organization of: Eagle I is parent organization of: Oregon Health and Science University Integrated Genomics Laboratory Core Facility is parent organization of: Oregon Health and Science University Multiscale Microscopy Core Facility is parent organization of: Oregon Health and Science University Elemental Analysis Core Facility is parent organization of: Oregon Health and Science University Center for Radiochemistry Research Core Facility is parent organization of: Oregon Health and Science University Biophysics Core Facility is parent organization of: Oregon Health and Science University Small Animal Research Imaging Core Facility is parent organization of: Oregon Health and Science University Biostatistics and Design Program Core Facility is parent organization of: Oregon Health and Science University Medicinal Chemistry Core Facility is parent organization of: Oregon Health and Science University Bioinformatics and Biostatistics Core Facility is parent organization of: MONARCH Initiative is parent organization of: Oregon Health and Science University Primate Genetics Core Facility is parent organization of: OHSU Monoclonal Antibody Shared Resource Core Facility |
nlx_80843, grid.5288.7, Crossref funder ID:100006668, Wikidata:Q282097, ISNI:0000 0000 9758 5690 | https://ror.org/009avj582 | SCR_009665 | Oregon Health & Science University; Oregon; USA, Oregon Health & Science University, Oregon Health University | 2026-08-08 11:59:24 | 1 | ||||||||
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U.S. Department of Commerce Resource Report Resource Website 1+ mentions |
U.S. Department of Commerce (RRID:SCR_009859) | Commerce.gov | institution | Executive department of the federal government concerned with promoting economic growth. Among its tasks are gathering economic and demographic data for business and government decision-making, and helping to set industrial standards. | Government granting agency |
is parent organization of: NIST - National Institute of Standards and Technology is parent organization of: National Oceanic and Atmospheric Administration is parent organization of: U.S. Census Bureau |
Crossref funder ID: 100000190, grid.239119.1, ISNI: 0000 0004 0478 6426, Wikidata: Q503577, nlx_144074 | https://ror.org/04chq2495 | SCR_009859 | United States Department of Commerce | 2026-08-08 11:59:24 | 2 | |||||||
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U.S. Geological Survey Resource Report Resource Website 500+ mentions |
U.S. Geological Survey (RRID:SCR_010168) | USGS | institution | Scientific agency of the United States government. The scientists of the USGS study the landscape of the United States, its natural resources, and the natural hazards that threaten it. The organization's work spans the disciplines of biology, geography, geology, and hydrology. | Government granting agency | nlx_157935, grid.2865.9, ISNI: 121546924, Crossref funder ID: 100000203, Wikidata: Q193755 | https://ror.org/035a68863 | SCR_010168 | United States Geological Survey | 2026-08-08 11:59:27 | 538 | ||||||||
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Common Terminology Criteria for Adverse Events Resource Report Resource Website 10+ mentions |
Common Terminology Criteria for Adverse Events (RRID:SCR_010296) | CTCAE | ontology, data or information resource, controlled vocabulary | A coding system for reporting adverse events that occur in the course of cancer therapy. It was derived from the Common Toxicity Criteria (CTC) v2.0 and is maintained by the Cancer Therapy Evaluation Program (CTEP) at the National Cancer Institution (NCI). | owl |
is listed by: BioPortal has parent organization: National Cancer Institute |
Cancer | nlx_157370 | SCR_010296 | 2026-08-08 11:59:26 | 14 | ||||||||
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University of Lyon; France Resource Report Resource Website 1+ mentions |
University of Lyon; France (RRID:SCR_010178) | university | University of Lyon, located in Lyon and Saint-Étienne, France, is a center for higher education and research comprising 11 members and 24 associated institutions. | is parent organization of: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France | nlx_30442 | http://www.univ-lyon2.fr/international-/ | SCR_010178 | 2026-08-08 11:59:17 | 1 | ||||||||||
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Amphibian Gross Anatomy Ontology Resource Report Resource Website 1+ mentions |
Amphibian Gross Anatomy Ontology (RRID:SCR_010291) | AAO | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon. | obo | is listed by: BioPortal | nlx_157316 | SCR_010291 | 2026-08-08 11:59:28 | 1 | |||||||||
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San Diego State University; California; USA Resource Report Resource Website 1+ mentions |
San Diego State University; California; USA (RRID:SCR_009874) | SDSU | university | Public research university in San Diego, California. Founded in 1897 as San Diego Normal School, it is the third-oldest university in the 23-member California State University system. | is parent organization of: PRINSEQ | nlx_156724, Wikidata:Q913861, ISNI:0000 0001 0790 1491, Crossref funder ID:100007099, grid.263081.e | https://ror.org/0264fdx42 | SCR_009874 | San Diego State University | 2026-08-08 11:59:16 | 1 | ||||||||
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IsoEM Resource Report Resource Website 10+ mentions |
IsoEM (RRID:SCR_009993) | IsoEM | software resource | Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Connecticut; Connecticut; USA |
biotools:isoem, OMICS_01278 | https://bio.tools/isoem | SCR_009993 | 2026-08-08 11:59:27 | 10 | ||||||||
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Centre for Reviews and Dissemination Resource Report Resource Website 10+ mentions |
Centre for Reviews and Dissemination (RRID:SCR_010267) | CRD | institution | A research department of the University of York provides research-based information about the effects of health and social care interventions via their databases. The institute undertakes systematic reviews evaluating research evidence on health and public health questions of national and international importance. | evidence review, research review, public health, evidence synthesis, FASEB list | is related to: PROSPERO | National Institute for Health Research UK | Public, Available to the research community | nlx_156926 | http://www.york.ac.uk/ | SCR_010267 | University of York Centre for Reviews and Dissemination | 2026-08-08 11:59:28 | 40 | |||||
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Phyre Resource Report Resource Website 500+ mentions |
Phyre (RRID:SCR_010270) | algorithm | A structure prediction system to reliably detect remote homologies. | has parent organization: Imperial College London; London; United Kingdom | PMID:19247286 | nlx_156932 | SCR_010270 | Protein Homology/Anology Recognition Engine | 2026-08-08 11:59:26 | 758 |
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