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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Turbo-BrainVoyager Resource Report Resource Website 1+ mentions |
Turbo-BrainVoyager (RRID:SCR_014175) | data processing software, standalone software, software resource, software application, image analysis software, data visualization software | A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal). | image analysis software, data visualization software, standalone software, neurofeedback, mri analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: BrainVoyager has parent organization: Brain Innovation: Home of the BrainVoyager Product Family |
Public, Commercial | http://www.brainvoyager.com/TurboBrainVoyager.html | SCR_014175 | 2026-08-04 09:43:21 | 2 | |||||||||
|
Topographica Resource Report Resource Website 1+ mentions |
Topographica (RRID:SCR_014174) | simulation software, software application, software resource | A software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project. Topographica focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. The software package provides a general-purpose framework for building models at this level, at an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation. It is intended to complement low-level neuron simulators that are available, such as General Neural Simulation System and NEURON. | computational modeling, neural map, simulation software, neuron |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: General Neural Simulation System is related to: NEURON |
NIMH Human Brain Project 1R01-MH66991 | SCR_014174 | 2026-08-04 09:43:22 | 5 | ||||||||||
|
Displacement Field Viewer Resource Report Resource Website |
Displacement Field Viewer (RRID:SCR_014101) | data processing software, data visualization software, software application, software resource | A tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field, a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Other key features include: view synchronization, adjustable mesh resolution, and conversion from deformation and HAMMER displacement fields. | data visualization software, displacement field, mesh, vector, field visualization |
uses: Insight Segmentation and Registration Toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Available for download, Free for non-commercial use | http://www.nitrc.org/plugins/mwiki/index.php/dfviewer:MainPage | SCR_014101 | DFViewer | 2026-08-04 09:43:20 | 0 | ||||||||
|
Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) Resource Report Resource Website 10+ mentions |
Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) (RRID:SCR_014186) | FRIEND | data processing software, standalone software, software resource, software application, image processing software | A GUI-based software for real-time fMRI processing, multivoxel pattern decoding and neurofeedback. The package integrates routines for image preprocessing in real-time, ROI-based feedback and brain decoding-based feedback using the FSL and libSVM libraries. Users can create or employ pre-specified visual stimuli for neurofeedback experiments. FRIEND can be used as Windows standalone software or as a multiplatform toolbox (called FRIEND Engine). | real time, fmri, processing, neuro feedback, standalone software, toolbox, |
uses: FSL uses: LIBSVM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Public, Available to the research community, The community can contribute to this resource | SCR_014186 | 2026-08-04 09:43:21 | 12 | |||||||||
|
Functional Mixed Processes Models Resource Report Resource Website |
Functional Mixed Processes Models (RRID:SCR_014187) | FMPM | data processing software, data analysis software, software resource, software application, workflow software | A tool which implements a functional analysis pipeline for the joint analysis of longitudinally measured functional data and clinical data (for example age, gender and disease status). FMPM consists of a functional mixed effects model for characterizing the association of functional response with covariates of interest by incorporating complex spatial–temporal correlation structure, an efficient method for spatially smoothing varying coefficient functions, an estimation method for estimating the spatial– temporal correlation structure, a test procedure with local and global test statistics for testing hypotheses of interest associated with functional response, and a simultaneous confidence band for quantifying the uncertainty in the estimated coefficient functions. | workflow software, data analysis software, analysis pipeline, longitudinal, functional data, clinical data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | SCR_014187 | 2026-08-04 09:43:21 | 0 | |||||||||
|
XNBC Resource Report Resource Website |
XNBC (RRID:SCR_014182) | simulation software, software application, software resource | A full featured and extensible application which simulates biological neural networks using graphic tools which edit neurons and networks, run the simulation and analyze results. It is written in C and runs on Unix and Windows. It is specifically targeted for neuroscientists who are less experienced with computer programming. | simulation software, biological neuron network, neuron, graphic tool, unexperienced programmer, unexperienced with computers |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Sorbonne University; Paris; France |
Available to the research community | http://ticemed-sa.upmc.fr/xnbc/ | SCR_014182 | 2026-08-04 09:43:22 | 0 | |||||||||
|
Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations Resource Report Resource Website 1+ mentions |
Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations (RRID:SCR_014168) | data or information resource, image collection | This resource provides simulated DW-MRI brain images and quantitative tools for evaluating the performance of diffusion analysis methods in terms of fiber orientation estimation and false-positive/-negative fiber rates, which are of fundamental importance to tractography based studies. DW data was generated using a multi-tensor model at SNRs of 9, 18 and 36, for sets of 20, 30, 40, 60, 90 and 120 gradient directions. For each combination of SNR and gradient direction set, 10 realizations of data are provided. All data is simulated with a diffusion-weighting of b=1000, as is common for clinical acquisitions. | brain image, dw mri, diffusion analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | SCR_014168 | 2026-08-04 09:43:21 | 1 | |||||||||||
|
Prediction and Diagnosis for Depression and Schizophrenia Resource Report Resource Website |
Prediction and Diagnosis for Depression and Schizophrenia (RRID:SCR_014161) | topical portal, portal, data or information resource | A topical portal for the UAIS Lab of Lanzhou University which researches predicting depression and schizophrenia based on demographics and physiological information (EEG, ERPs, Genetics, MRI, fMRI, etc.). It also researches wearable bio-signal sensors and antennas, bio-signal processing, speech analysis, pervasive mental health, psycho-physiological computing, bioinformatics and multimodal data fusion and modeling. | topical portal, lab, depression, schizophrenia, demographic, physiological | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Depression, Schizophrenia | Public | http://www.nitrc.org/projects/zhangxw | SCR_014161 | UAIS Lab of Lanzhou University | 2026-08-04 09:43:21 | 0 | |||||||
|
vini: A viewer for fMRI data Resource Report Resource Website |
vini: A viewer for fMRI data (RRID:SCR_017250) | data processing software, data visualization software, software application, software resource | Software Python tool as viewer for MRI data and numpy arrays. | viewer, MRI, data, numpy, array | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/lipsia-fmri/vini | SCR_017250 | 2026-08-04 09:44:09 | 0 | |||||||||
|
Diffusion Toolkit Resource Report Resource Website 50+ mentions |
Diffusion Toolkit (RRID:SCR_017345) | DTK | data processing software, software application, software resource, data analysis software | Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography. | data, reconstruction, fiber, tracking, diffusion, MR, image, processing, tractography |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard University; Cambridge; United States |
Restricted | https://cds.ismrm.org/ismrm-2007/files/03720.pdf, https://www.nitrc.org/projects/trackvis/ | SCR_017345 | 2026-08-04 09:44:09 | 55 | ||||||||
|
MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, software resource, web service | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://localiview.apps.ebrains.eu/, https://meshview-for-brain-atlases.readthedocs.io, https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases | SCR_017222 | MeshView for brain atlases | 2026-08-04 09:44:06 | 11 | ||||||
|
Knowing what you know (kwyk) - Bayesian Brain Parcellation Resource Report Resource Website |
Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) | kwyk | segmentation software, data processing software, software resource, software application, image analysis software | Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation. | Deep, neural, network, prediction, FreeSurfer, segmentation, structural, MRI, volume, brain, parcellation, uncertainty, estimation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/neuronets/kwyk | SCR_017470 | knowing what you know | 2026-08-04 09:44:10 | 0 | |||||||
|
MonkeyCBP Resource Report Resource Website 1+ mentions |
MonkeyCBP (RRID:SCR_017640) | MonkeyCBP | software toolkit, software resource, algorithm resource | Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community. | MonkeyCBP, Atlas, Parcellation Atlas, neuroimaging pipeline, brain, | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | SCR_017675 | http://www.nitrc.org/projects/monkey-cbp/ | SCR_017640 | Monkey Connectivity Based Parcellation; MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain | 2026-08-04 09:44:12 | 1 | ||||||
|
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, software application, image processing software, 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 | 2026-08-04 09:42:26 | 1 | |||||
|
GIFTI Resource Report Resource Website 10+ mentions |
GIFTI (RRID:SCR_009579) | GIfTI | software resource, narrative resource, data or information 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 | 2026-08-04 09:42:24 | 28 | |||||||||
|
DOTS WM tract segmentation Resource Report Resource Website 100+ mentions |
DOTS WM tract segmentation (RRID:SCR_009459) | DOTS | segmentation software, data processing software, software resource, software application, image analysis software | A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance, diffusion tensor mr imaging, dti, fiber tract, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MIPAV: Medical Image Processing and Visualization is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
NIDA K25DA025356 | PMID:21718790 | Free | nlx_155605 | SCR_009459 | Diffusion-Oriented Tract Segmentation White Matter tract segmentation, Diffusion-Oriented Tract Segmentation | 2026-08-04 09:42:23 | 115 | |||||
|
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 | 2026-08-04 09:42:25 | 0 | |||||||
|
Neuroimaging Made Easy Blog Resource Report Resource Website |
Neuroimaging Made Easy Blog (RRID:SCR_009611) | Neuroimaging Made Easy | software resource, blog, narrative resource, data or information 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 | 2026-08-04 09:42:26 | 0 | |||||||
|
ERPLAB Resource Report Resource Website 100+ mentions |
ERPLAB (RRID:SCR_009574) | ERPLAB | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:42:25 | 428 | |||||
|
EMSE Suite Resource Report Resource Website 10+ mentions |
EMSE Suite (RRID:SCR_009571) | EMSE Suite | data processing software, software resource, software application, image analysis software, 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 | 2026-08-04 09:42:25 | 10 |
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.
