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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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OEI: fMRI compatible olfactometer Resource Report Resource Website 1+ mentions |
OEI: fMRI compatible olfactometer (RRID:SCR_002507) | OEI fMRI compatible olfactometer | instrument resource | A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory. | experiment control, hardware, magnetic resonance, stimulus presentation, odor, olfactory, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_002507.pdf | nlx_155907 | http://www.nitrc.org/projects/oei, http://www.osmicenterprises.com/docs/OsmicFMRIOlfactomterManual%207-1-13.pdf | SCR_002507 | SciCrunch Registry | 2026-09-26 02:13:13 | 4 | ||||||
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Non-Rigid Image Registration Evaluation Project Resource Report Resource Website 1+ mentions |
Non-Rigid Image Registration Evaluation Project (RRID:SCR_002505) | NIREP | data or information resource, database, narrative resource, software resource, standard specification | Project to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria. The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms. | magnetic resonance, registration software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Iowa; Iowa; USA |
NIBIB R33 EB004126 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155904 | http://www.nitrc.org/projects/nirep | SCR_002505 | SciCrunch Registry | Non-Rigid Image Registration Evaluation Project, Non-Rigid Image Registration Evaluation Project (NIREP) | 2026-09-26 02:13:13 | 7 | |||||
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S-rep Fitting Statistics and Segmentation Resource Report Resource Website |
S-rep Fitting Statistics and Segmentation (RRID:SCR_002540) | S-rep Fitting Statistics and Segmentation | data processing software, image analysis software, segmentation software, software application, software resource | Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed. | computational neuroscience, computed tomography, domain independent, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155948 | SCR_002540 | SciCrunch Registry | 2026-09-26 02:13:14 | 0 | ||||||||
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Grants.gov Resource Report Resource Website 10+ mentions |
Grants.gov (RRID:SCR_002661) | funding resource | A source to FIND and APPLY for federal grants. The U.S. Department of Health and Human Services is proud to be the managing partner for Grants.gov, an initiative that is having an unparalleled impact on the grant community. All discretionary grants offered by the 26 federal grant-making agencies can be found on Grants.gov. Grants.gov was established as a governmental resource named the E-Grants Initiative, part of the President's 2002 Fiscal Year Management Agenda to improve government services to the public. The concept has its origins in the Federal Financial Assistance Management Improvement Act of 1999, also known as Public Law 106-107. Public Law 106-107 has since sunset and is now known as the Grants Policy Committee (GPC). For more information on the Grants Policy Committee, click here. Today, Grants.gov is a central storehouse for information on over 1,000 grant programs and provides access to approximately $500 billion in annual awards. You may find information on *What is a Grant? *Who is Eligible for a Grant? *Program highlights and accomplishments *Grants.gov in the News (Articles, press releases, milestones and events) *Program Status (Detailed information about our relationship with partner federal agencies, financial contributions, grant opportunities, fiscal reports, planning strategies and statistics.) | grant, funding, award, database, opportunity |
is used by: NIF Data Federation is used by: Aging Portal is used by: NIDDK Information Network (dkNET) |
Free, Freely available | nif-0000-22393 | SCR_002661 | SciCrunch Registry | 2026-09-26 02:13:15 | 36 | |||||||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, data processing software, software application, software resource | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SciCrunch Registry | SCRalyze - A matlab environment for model-based psychophysiology | 2026-09-26 02:13:13 | 17 | ||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | data or information resource, discussion, knowledge environment, narrative resource | Project to discuss, debate, develop and deploy ontological practices for the fMRI community. | community, ontology, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155943 | SCR_002536 | SciCrunch Registry | 2026-09-26 02:13:13 | 0 | ||||||||
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Cancer Genomics Hub Resource Report Resource Website 100+ mentions |
Cancer Genomics Hub (RRID:SCR_002657) | CGHub | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer. | genome, genome sequence, alignment, mutation | has parent organization: University of California at Santa Cruz; California; USA | Cancer | PMID:25267794 | THIS RESOURCE IS NO LONGER IN SERVICE. | r3d100011174, nlx_156095 | https://doi.org/10.17616/R3F919 | SCR_002657 | SciCrunch Registry | 2026-09-26 02:13:15 | 179 | |||||
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MCML and CONV Resource Report Resource Website |
MCML and CONV (RRID:SCR_002419) | MCML, MCML & CONV, CONV | simulation software, software application, software resource | MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications. | optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Oregon Health and Science University; Oregon; USA |
PMID:9421660 PMID:19256707 |
Free, Available for download, Freely available | nlx_155791 | http://www.nitrc.org/projects/mcml | SCR_002419 | SciCrunch Registry | Monte Carlo for Multi-Layered media | 2026-09-26 02:13:12 | 0 | |||||
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Rodent Cortical Thickness Analysis Resource Report Resource Website |
Rodent Cortical Thickness Analysis (RRID:SCR_002539) | data processing software, image analysis software, image processing software, software application, software resource | An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling | microscopy, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155946 | http://www.nitrc.org/projects/rodentthickness | SCR_002539 | SciCrunch Registry | RodentThickness | 2026-09-26 02:13:13 | 0 | |||||||
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Quick-R Resource Report Resource Website 1+ mentions |
Quick-R (RRID:SCR_002417) | Quick-R | book, data or information resource, narrative resource, training material | Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it. | r, programming language, code | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01760 | SCR_002417 | SciCrunch Registry | Quick-R - accessing the power of R | 2026-09-26 02:13:12 | 5 | |||||||
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Rodent Brain Extraction Tool Resource Report Resource Website |
Rodent Brain Extraction Tool (RRID:SCR_002538) | rBET | data processing software, image processing software, software application, software resource | A modified version of the Brain Extraction Tool (BET) that can process rodent brains. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: King's College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_155945 | http://www.nitrc.org/projects/rbet | SCR_002538 | SciCrunch Registry | 2026-09-26 02:13:13 | 0 | |||||||
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PaleoVu Resource Report Resource Website |
PaleoVu (RRID:SCR_002411) | PaleoVu | data processing software, data visualization software, software application, software resource | A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data. | browse, visualization, paleo, paleoclimatology, ecology, paleoclimate, climate, query, windows, macintosh, paleoecological |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
Free | SciRes_000130 | SCR_002411 | SciCrunch Registry | 2026-09-26 02:13:12 | 0 | ||||||||
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Pythagorean Displacement and Motion Regressors Resource Report Resource Website 1+ mentions |
Pythagorean Displacement and Motion Regressors (RRID:SCR_002525) | Pythagorean Displacement and Motion Regressors | software resource | Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment. | algorithm, magnetic resonance, matlab, pythagorean theorem, head, motion, position, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155931 | SCR_002525 | SciCrunch Registry | 2026-09-26 02:13:13 | 5 | ||||||||
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PySurfer Resource Report Resource Website 10+ mentions |
PySurfer (RRID:SCR_002524) | PySurfer | data processing software, data visualization software, software application, software library, software resource, software toolkit | Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155930 | http://www.nitrc.org/projects/pysurfer, https://sources.debian.org/src/python3-surfer/ | SCR_002524 | SciCrunch Registry | 2026-09-26 02:13:13 | 29 | |||||||
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RDFaCE Resource Report Resource Website |
RDFaCE (RRID:SCR_002645) | RDFaCE | authoring tool, software application, software resource | A Semantic content editor based on TinyMCE WYSIWYG editor. RDFaCE is created as a proof of concept for WYSIWYM (What You See Is What You Mean) concept. WYSIWYM aims to enable end-users to easily annotate their content using RDFa and Microdata markups. RDFaCE employs external NLP APIs to suggest namespaces, properties, URIs and to automatically annotate content. | annotation, authoring, markup, rdfa |
is listed by: FORCE11 has parent organization: University of Leipzig; Saxony; Germany |
Free, Available for download, Freely available | nlx_156074 | SCR_002645 | SciCrunch Registry | RDFa Content Editor | 2026-09-26 02:13:15 | 0 | |||||||
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ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | data analysis software, data processing software, sequence analysis software, simulation software, software application, software resource | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | SciCrunch Registry | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-09-26 02:13:13 | 35 | ||||||
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ModelGUI Resource Report Resource Website 1+ mentions |
ModelGUI (RRID:SCR_002441) | mgui | data processing software, data visualization software, rendering software, software application, software resource | An open source Java-based project intended to provide a graphic user interface (GUI) for interactions between scientists (or enthusiasts) and their data. In its current (beta) form, mgui offers the following functionality: * Cross-platform functionality (with a Java Runtime installation, runs on Linux, Windows, Mac, or Solaris) * 2D rendering of data based upon Java2D, and 3D rendering based upon Java3D * The ability to organize complex datasets into intuitive mgui projects * A processing pipeline interface which allows users to process their datasets with any available Java or native software tools * An extensible I/O framework accommodating a variety of standard and non-standard file formats * Database connectivity using JDBC * Graph visualization based upon the JUNG library * An intuitive Swing-based GUI for managing, querying, and visualizing data * Various CAD-type tools for editing and creating geometry * A computational modelling framework | clipping, database application, domain independent, gifti, image display, java, nifti, os independent, platform, development environment, rendering, surface rendering, three dimensional display, two dimensional display, visualization, volume rendering, java | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155816 | http://www.nitrc.org/projects/modelgui | SCR_002441 | SciCrunch Registry | 2026-09-26 02:13:12 | 1 | |||||||
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Spanish Resting State Network Resource Report Resource Website |
Spanish Resting State Network (RRID:SCR_002562) | SRSN | community building portal, data or information resource, portal | Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.) | microsoft word document, magnetic resonance, nifti, pdf, spanish |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 1000 Functional Connectomes Project |
Free | nlx_155968 | SCR_002562 | SciCrunch Registry | 2026-09-26 02:13:14 | 0 | ||||||||
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flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | SciCrunch Registry | flowBeads: Analysis of flow bead data | 2026-09-26 02:13:12 | 0 | ||||||||
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MultiTracer Resource Report Resource Website 10+ mentions |
MultiTracer (RRID:SCR_002445) | MultiTracer | data processing software, data visualization software, software application, software resource | A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set. | analyze, computed tomography, image display, java, manual, magnetic resonance, nifti, os independent, pet, spect, region growing, segmentation, three dimensional display, two dimensional display, visualization, volumetric analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA has parent organization: Laboratory of Neuro Imaging |
PMID:12948737 | Free, Available for download, Freely available | nlx_155819 | http://www.nitrc.org/projects/multitracer2 | SCR_002445 | SciCrunch Registry | MultiTracer version 2 | 2026-09-26 02:13:12 | 11 |
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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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