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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-21 12:38:56 | 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, image analysis software, software application, software resource, software toolkit | 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 | 2026-08-21 12:39:02 | 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, image analysis software, registration software, software application, software resource | 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 | 2026-08-21 12:38:46 | 0 | ||||||||
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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 | 2026-08-21 12:38:53 | 2 | ||||||
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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 | 2026-08-21 12:39:06 | 1004 | ||||
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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 | 2026-08-21 12:38:56 | 0 | ||||||||
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DTI BrainImageScope Resource Report Resource Website |
DTI BrainImageScope (RRID:SCR_009559) | dtiBrainScope | data processing software, image processing software, software application, software resource | Software package for processing diffusion tensor imaging data. The following functions are included: 1. Converting imaging data in DICOME format to ANALYZE format 2. Extracting binary brain mask for quick scalp-removing 3. Correcting eddy-current induced distortion 4. Optimized tensor estimation based on noisy diffusion-weighted imaging (DWI) data 5. Scalp removal using a brain mask image 6. Corregistering imaging data and generating deformation field for mapping images from individual spaces to a template or target space 7. Spatial Normalization and Warping DTI 8. Fiber tracking 9. Clustering fiber tracts 10. Identifying brain ventricles and generating binary masks for the baseline and DW imaging data 11. Deriving diffusion anisotropy indices (DAIs) and principal directions (PD) and the corresponding color-coded PD-map. | magnetic resonance, diffusion tensor imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: Columbia University; New York; USA |
NIBIB 1R03EB008235-01A1; Shanghai CST 10440710200 |
Other/Commercial license License | nlx_155739 | SCR_009559 | 2026-08-21 12:38:47 | 0 | |||||||
|
CoCoMac-Paxinos3D viewer Resource Report Resource Website |
CoCoMac-Paxinos3D viewer (RRID:SCR_009548) | CoCoMac-Paxinos3D viewer | data processing software, data visualization software, software application, software resource | An interactive interface of macaque stereotaxic atlas with a connectivity database, allowing integrated data analysis and mapping between 3D structures with database vocabularies. These Java-based tools are capable of reading stacks of polygons described in svg vector format and arrange them in 3D space so that the corresponding structures can be viewed and manipulated individually. An additional excel (currently v. 1997-2003) file maintains the structure abbreviations and their mapping to the terminology of databases that provide supplementary information. Here in particular we have manually drawn the cortical, striatal, thalamic and amygdaloid structures of the 151 frontal sections from the Rhesus Monkey Brain in Stereotactic Coordinates authored by Paxinos and colleagues in 1999. After loading the excel file and a set of the svg files, the view can be rotated, zoomed and individual brain structures be selected for identification and simple geometric measures. A stereotaxic grid is a display option. The abbreviations of the brain structures are mapped to entities recorded in the CoCoMac database of primate brain connectivity. Thereby one can retrieve mapping and connectivity information for the selected structure as text or connecting arrows. | magnetic resonance, java, mapping, connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: CoCoMac |
PMID:19145492 | GNU General Public License | nlx_155728 | http://www.nitrc.org/projects/cp3d | SCR_009548 | 2026-08-21 12:39:03 | 0 | ||||||
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INVIZIAN Resource Report Resource Website 1+ mentions |
INVIZIAN (RRID:SCR_009549) | INVIZIAN | data processing software, data visualization software, software application, software resource | 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 | 2026-08-21 12:38:47 | 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 | 2026-08-21 12:38:51 | 2 | |||||||
|
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 | 2026-08-21 12:39:19 | 538 | ||||||||
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Biodiversity Ontology Resource Report Resource Website |
Biodiversity Ontology (RRID:SCR_010204) | BOF | controlled vocabulary, data or information resource, ontology | An ontology of biodiversity of INPA | owl | is listed by: BioPortal | nlx_157331 | SCR_010204 | 2026-08-21 12:39:12 | 0 | |||||||||
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Cognitive Atlas Ontology Resource Report Resource Website |
Cognitive Atlas Ontology (RRID:SCR_010295) | COGAT | controlled vocabulary, data or information resource, ontology | Ontology that characterizes the state of current thought in cognitive science. It defines a set of mental concepts along with a set of mental tasks, and the measurement relations between those classes. | owl |
is listed by: BioPortal has parent organization: Cognitive Atlas |
nlx_157368 | SCR_010295 | 2026-08-21 12:38:59 | 0 | |||||||||
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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 | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-21 12:39:15 | 14 | ||||||||
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Comparative Data Analysis Ontology Resource Report Resource Website |
Comparative Data Analysis Ontology (RRID:SCR_010297) | CDAO | controlled vocabulary, data or information resource, ontology | A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science | owl, biology, evolution, computer science, comparative analysis, phylogenetic tree, operational taxonomic unit, compared character, molecular |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge |
Public domain | nlx_157371 | http://purl.bioontology.org/ontology/CDAO, http://purl.obolibrary.org/obo/cdao.owl | SCR_010297 | 2026-08-21 12:39:21 | 0 | |||||||
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Content Archive Resource Exchange Lexicon Resource Report Resource Website |
Content Archive Resource Exchange Lexicon (RRID:SCR_010298) | CARELEX | controlled vocabulary, data or information resource, ontology | Categories and terms used to classify content (documents, images, etc) in electronic content repositories for life science / BioPharma. Initial version contains content model for use with clinical trial electronic Trial Master Files or eTMF archives. A Content model contains content classification categories (classes) and metadata properties (data properties). Data properties should be assigned to each Content Type. Recent changes include: addition of electronic signature support, medical imaging classifications. | owl | is listed by: BioPortal | nlx_157377 | http://www.carelex.org | SCR_010298 | 2026-08-21 12:38:59 | 0 | ||||||||
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Amphibian Gross Anatomy Ontology Resource Report Resource Website 1+ mentions |
Amphibian Gross Anatomy Ontology (RRID:SCR_010291) | AAO | controlled vocabulary, data or information resource, ontology | 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 | 2026-08-21 12:39:20 | 1 | |||||||||
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Disease core ontology applied to Rare Diseases Resource Report Resource Website |
Disease core ontology applied to Rare Diseases (RRID:SCR_010308) | HRDO | controlled vocabulary, data or information resource, ontology | A core ontology consistent with a metamodel (disorders and groups of disorders, genes, clinical signs and their relations) and an instantiation of this metamodel with Orphanet Data (available on http://orphadata.org). Research experiments demonstrated (i) efficient classifications generation based on SPARQL Construct, (ii) perspectives in semantic audit of a knowledge base, (iii) semantic comparison with OMIM (www.omim.org) using proximity measurements and (iv) opened perspectives in knowledge sharing (LORD, http://lord.bndmr.fr). Current production services of Orphanet developed ORDO, released in 2014, an ontology synchronized with their production database. | owl |
is listed by: BioPortal is related to: Orphanet |
INSERM | nlx_157388 | SCR_010308 | 2026-08-21 12:39:16 | 0 | ||||||||
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Current Procedural Terminalogy Hierarchy Resource Report Resource Website |
Current Procedural Terminalogy Hierarchy (RRID:SCR_010300) | CPTH | controlled vocabulary, data or information resource, ontology | Metathesaurus of current procedural terminalogy (CPT). | umls | is listed by: BioPortal | nlx_157379 | SCR_010300 | 2026-08-21 12:39:21 | 0 | |||||||||
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Dengue Fever Ontology Resource Report Resource Website |
Dengue Fever Ontology (RRID:SCR_010304) | IDODEN | controlled vocabulary, data or information resource, ontology | An ontology for dengue fever. | owl | is listed by: BioPortal | Dengue fever | nlx_157383 | http://code.google.com/p/dengue-fever-ontology/ | SCR_010304 | 2026-08-21 12:38:59 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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