Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Corpus Callosum Thickness Profile Analysis Pipeline Resource Report Resource Website |
Corpus Callosum Thickness Profile Analysis Pipeline (RRID:SCR_003575) | ccsegthickness | software resource | An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python. | linux, matlab, mr, nifti-1, posix/unix-like, corpus callosum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:24968872 | GNU General Public License | nlx_157716 | SCR_003575 | 2026-02-07 02:06:23 | 0 | |||||||
|
Multicomponent T2 estimation with stimulated echo correction Resource Report Resource Website |
Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) | Multicomponent T2 estimation with stimulated echo correction | software resource | Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches. | algorithm, matlab, magnetic resonance, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:23629849 | Free, Available for download, Freely available | nlx_155820 | SCR_002446 | 2026-02-07 02:05:44 | 0 | |||||||
|
COGNISION Resource Report Resource Website 1+ mentions |
COGNISION (RRID:SCR_002362) | COGNISION | software resource | A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker). | eeg, eeg, meg, electrocorticography, event-related potentials, hardware, physiological recording, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155724 | http://www.nitrc.org/projects/neuronetrix | SCR_002362 | COGNISION (TM) System | 2026-02-07 02:05:54 | 2 | ||||||
|
NiBabel Resource Report Resource Website 100+ mentions |
NiBabel (RRID:SCR_002498) | NiBabel | software resource | A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI. | magnetic resonance, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PyNIfTI is related to: MNE software has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155896 | http://www.nitrc.org/projects/nibabel | SCR_002498 | NIPY File IO | 2026-02-07 02:05:56 | 109 | ||||||
|
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 | 2026-02-07 02:05:45 | 5 | ||||||||
|
Signed Differential Mapping Resource Report Resource Website 100+ mentions |
Signed Differential Mapping (RRID:SCR_002554) | SDM | software resource | Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera). | magnetic resonance, pet, spect, fmri, vbm, meta-analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155962 | http://www.nitrc.org/projects/sdm | SCR_002554 | 2026-02-07 02:05:46 | 145 | |||||||
|
Triangle BioSystems Resource Report Resource Website 10+ mentions |
Triangle BioSystems (RRID:SCR_002603) | TBSI | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software | computational neuroscience, eeg, eeg, meg, electrocorticography, hardware, other software resource, physiological recording, software | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156006 | http://www.nitrc.org/projects/tbsi | SCR_002603 | Triangle BioSystems International | 2026-02-07 02:05:46 | 11 | ||||||
|
TetraMetrix Resource Report Resource Website 1+ mentions |
TetraMetrix (RRID:SCR_002601) | TetraMetrix | software resource | An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left. | magnetic resonance, 3d, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
Free, Available for download, Freely available | nlx_156004 | SCR_002601 | 2026-02-07 02:05:58 | 1 | ||||||||
|
PennCNV Resource Report Resource Website 100+ mentions |
PennCNV (RRID:SCR_002518) | PennCNV | software resource | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm. | imaging genomics, copy number variation, snp, genotyping array, array, oligonucleotide, hidden markov model, genotype, genome |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VegaMC is related to: OpenBioinformatics.org has parent organization: University of Pennsylvania; Philadelphia; USA |
NIMH MH604687 | PMID:17921354 | Free | OMICS_00729, nlx_155921 | http://www.openbioinformatics.org/penncnv/ |
http://www.neurogenome.org/cnv/penncnv | SCR_002518 | PennCNV: copy number variation detection | 2026-02-07 02:05:45 | 339 | |||
|
Web Interfaces for Multiscale Images Resource Report Resource Website |
Web Interfaces for Multiscale Images (RRID:SCR_002589) | Web Interfaces for Multiscale Images | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web. | magnetic resonance, interoperability, microscopy, standard specification, forum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156020 | SCR_002589 | 2026-02-07 02:05:46 | 0 | ||||||||
|
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 | nlx_155907 | http://www.nitrc.org/projects/oei http://www.osmicenterprises.com/docs/OsmicFMRIOlfactomterManual%207-1-13.pdf |
SCR_002507 | 2026-02-07 02:05:57 | 3 | |||||||
|
EYE-EEG (combined eye-tracking & EEG) Resource Report Resource Website 10+ mentions |
EYE-EEG (combined eye-tracking & EEG) (RRID:SCR_012903) | EYE-EEG | software resource | A plugin for the open-source MATLAB toolbox EEGLAB developed with the goal to facilitate integrated analyses of electrophysiological and oculomotor data. The plugin parses, imports, and synchronizes simultaneously recorded eye tracking data and adds it as extra channels to the EEG. Saccades and fixations can be imported from the eye tracking raw data or detected with an adaptive velocity-based algorithm. Eye movements are then added as new time-locking events to EEGLAB's event structure, allowing easy saccade- and fixation-related EEG analysis (e.g., fixation-related potentials, FRPs). Alternatively, EEG data can be aligned to stimulus onsets and analyzed according to oculomotor behavior (e.g. pupil size, microsaccades) in a given trial. Saccade-related ICA components can be objectively identified based on their covariance with the electrically independent eye tracker. All functions can be accessed via EEGLAB's GUI or called from the command line. | eeg, meg, electrocorticography, matlab, os independent, eye, electrophysiology, oculomotor, eye tracking device |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Humboldt University of Berlin; Berlin; Germany |
DFG | PMID:21744985 | GNU General Public License | nlx_155755 | http://www.nitrc.org/projects/eye-eeg | SCR_012903 | EYE-EEG: Eye tracking & EEG | 2026-02-07 02:08:48 | 13 | ||||
|
BRAINSTracer Resource Report Resource Website 1+ mentions |
BRAINSTracer (RRID:SCR_012894) | BRAINSTracer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155705 | http://www.nitrc.org/projects/brainstracer | SCR_012894 | 2026-02-07 02:08:37 | 5 | |||||||
|
NiftySim Resource Report Resource Website 1+ mentions |
NiftySim (RRID:SCR_006591) | NiftySim | software resource | A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages. | pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
BSD License | nlx_155900 | http://www.nitrc.org/projects/niftysim | SCR_006591 | Nifty Sim | 2026-02-07 02:07:12 | 3 | ||||||
|
Web Game for Collaborative Labeling Resource Report Resource Website 1+ mentions |
Web Game for Collaborative Labeling (RRID:SCR_006685) | Web Game for Collaborative Labeling | software resource | Web game that provides an innovative infrastructure for labeling to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function. | magnetic resonance, labeling, crowdsourcing | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_156019 | http://www.nitrc.org/projects/webmill | SCR_006685 | 2026-02-07 02:07:32 | 2 | |||||||
|
BASH4RfMRI Resource Report Resource Website |
BASH4RfMRI (RRID:SCR_005970) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI. | algorithm or reusable library, information theory, spectral analysis, correlation, multivariate analysis, platform or development environment, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL is related to: Analysis of Functional NeuroImages is related to: FreeSurfer is related to: 1000 Functional Connectomes Project |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151343 | SCR_005970 | BASH Scripts, bash-rs-fcmri | 2026-02-07 02:07:01 | 0 | ||||||||
|
POLGUI - Matlab Polhemus Interface Resource Report Resource Website 1+ mentions |
POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) | POLGUI | software resource | An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows) | eeg, meg, electrocorticography, linux, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
BSD License | nlx_155915 | http://www.nitrc.org/projects/polgui | SCR_006752 | POLGUI - Matlab GUI for Polhemus Fastrak | 2026-02-07 02:07:15 | 3 | ||||||
|
DIAMOND Resource Report Resource Website 1000+ mentions |
DIAMOND (RRID:SCR_009457) | DIAMOND | software resource | Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans. | reusable library, analyze, database application, dicom, format conversion, image display, image reconstruction, magnetic resonance, nifti, python, software, visualization, workflow, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Davis; California; USA |
nlx_155603 | SCR_009457 | UC Davis IDeA Lab Applications for Management Of Neuroimaging Data | 2026-02-07 02:07:36 | 4151 | ||||||||
|
CBS High-Res Brain Processing Tools Resource Report Resource Website 10+ mentions |
CBS High-Res Brain Processing Tools (RRID:SCR_009452) | CBS High-Res Brain Processing Tools | software resource | A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit is related to: MIPAV: Medical Image Processing and Visualization |
Free | nlx_155596 | SCR_009452 | 2026-02-07 02:07:36 | 20 | ||||||||
|
Fiber Optic Button Response System Resource Report Resource Website 10+ mentions |
Fiber Optic Button Response System (RRID:SCR_009577) | instrument resource | Instrument that accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant?s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed. | eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, response monitoring, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155759 | http://www.nitrc.org/projects/fobrs https://pstnet.com/wp-content/uploads/2021/04/Celeritas-Operator-Manual.pdf |
SCR_009577 | Celeritas Fiber Optic Response System | 2026-02-07 02:07:54 | 22 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
