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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Lipsia Resource Report Resource Website 10+ mentions |
Lipsia (RRID:SCR_009595) | Lipsia | software application, software resource, data processing software, image processing software, image analysis software | Software tool for processing functional magnetic resonance imaging (fMRI) data.Software system for evaluation of functional magnetic resonance images of human brain. | magnetic resonance, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig; Germany |
PMID:11679206 | Free, Available for download, Freely available | nlx_155787 | http://www.nitrc.org/projects/lipsia, https://sources.debian.org/src/lipsia/ | SCR_009595 | Lipsia: Leipzig Image Processing and Statistical Inference Algorithms ? a tool for fMRI data analysis, Leipzig Image Processing and Statistical Inference Algorithms, Lipsia: Leipzig Image Processing and Statistical Inference Algorithms | 2026-07-28 09:42:20 | 39 | |||||
|
FBIRN Image Processing Scripts Resource Report Resource Website 1+ mentions |
FBIRN Image Processing Scripts (RRID:SCR_009471) | FIPS | software application, software resource, data management software | A FSL package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control. | analyze, csh/tcsh, database application, dicom, linux, macos, magnetic resonance, posix/unix-like, statistical operation, unix shell, web environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Function BIRN |
BIRN License, BSD License | nlx_155618 | SCR_009471 | FBIRN Image Processing Scripts (FIPS) | 2026-07-28 09:42:26 | 5 | |||||||
|
LIMO EEG Resource Report Resource Website 10+ mentions |
LIMO EEG (RRID:SCR_009592) | LIMO EEG | software application, image analysis software, software resource, data processing software, image processing software, software toolkit | A matlab toolbox (EEGlab compatible) allowing the processing of MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with the tool. Across subject analyses are performed using bootstrap offering robust inferences. | reusable library, application, eeg, meg, electrocorticography, matlab, os independent, time domain analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155782 | http://www.nitrc.org/projects/limo_eeg | SCR_009592 | 2026-07-28 09:42:27 | 10 | |||||||
|
Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI Resource Report Resource Website 1+ mentions |
Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI (RRID:SCR_009502) | software application, software resource, data processing software, image processing software, standalone software | This module reduces Rician noise on nhdr/nrrd DWIs. Filters image in mean squared error sense using Rician noise model. All estimations are performed as sample estimates in a "shaped neighborhood" defined by the weights extracted from structural similarity of voxels following same idea as in Non-Local Means filter. | reduce Rician noise, Rician noise model, image filter, |
uses: Insight Segmentation and Registration Toolkit is used by: 3D Slicer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Ministerio de Ciencia y Educacion ; Junta de Castilla y Leon |
Free, Available for download, Freely available | nlx_155649, SCR_014129 | SCR_009502 | Joint Anisotropic LMMSE Filter for Stationary Rici | 2026-07-28 09:42:18 | 1 | |||||||
|
JIP Analysis Toolkit Resource Report Resource Website 10+ mentions |
JIP Analysis Toolkit (RRID:SCR_009588) | JIP Toolkit | software application, software toolkit, software resource, data processing software, image analysis software | Software toolkit for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for fMRI time series analysis, a 1st-order GLM analysis for PET data within the SRTM framework, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 4) MRI templates to place your rodent and non-human primate data into standardized spaces. | affine warp, atlas application, atlas data, c, console (text based), image display, image-to-image, linux, macos, magnetic resonance, nifti, nonlinear warp, pet, spect, posix/unix-like, registration, resampling, spatial transformation, time domain analysis, visualization, warping, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard Medical School; Massachusetts; USA |
NIBIB R03EB008134 | MGH CSRL License | nlx_155778 | http://www.nitrc.org/projects/jip | SCR_009588 | JIP fMRI Analysis Toolkit | 2026-07-28 09:42:20 | 21 | |||||
|
DW-MRI registration in FSL Resource Report Resource Website 1+ mentions |
DW-MRI registration in FSL (RRID:SCR_009461) | DW-MRI registration in FSL | software application, software resource, data processing software, registration software, image analysis software | This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images (DW-MRIs) by extending FLIRT (linear registration of 3D scalar volumes) and FNIRT (non-linear registration of 3D scalar volumes) in the FMRIB Software Library (FSL) to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation (Tao, X., Miller, J. V., 2006. A method forregistering diffusion weighted magnetic resonance images. In: MICCAI. Vol. 9. pp. 594?602), which is implemented and extended to non-linear registration, based on the FLIRT and FNIRT models in FSL. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00041/abstract. The code does not overwrite FLIRT, FNIRT or any of the FSL C++ code. It is added as FLIRT4D, FNIRT4D and supporting cost functions. The makefiles will however be overwritten to compile the new code, without affecting any version of FSL. | magnetic resonance, diffusion weighted magnetic resonance image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL |
PMID:23596381 | FSL License | nlx_155607 | SCR_009461 | 2026-07-28 09:42:20 | 2 | |||||||
|
HAMMER Suite Resource Report Resource Website 1+ mentions |
HAMMER Suite (RRID:SCR_009583) | HAMMER Suite | software application, image analysis software, software resource, data processing software, image processing software, software toolkit | The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration. | magnetic resonance, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:12575879 | Free | nlx_155769 | http://www.nitrc.org/projects/hammer_suite | SCR_009583 | 2026-07-28 09:42:20 | 1 | ||||||
|
eConnectome Resource Report Resource Website 10+ mentions |
eConnectome (RRID:SCR_009618) | eConnectome | software application, software resource, data processing software, image processing software, image analysis software | An open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome La Sapienza. | eeg, meg, electrocorticography, forward - inverse, matlab, microsoft, modeling, multivariate analysis, region of interest, segmentation, statistical operation, visualization, windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIBIB RO1 EB006433; NIBIB RO1 EB007920 |
GNU General Public License | nlx_155844 | http://www.nitrc.org/projects/econnectome | SCR_009618 | Electrophysiological Connectome | 2026-07-28 09:42:20 | 30 | |||||
|
BrainMagix SPM Viewer Resource Report Resource Website 1+ mentions |
BrainMagix SPM Viewer (RRID:SCR_009537) | BrainMagix SPM Viewer | data visualization software, software resource, software application, 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 | 2026-07-28 09:42:27 | 1 | |||||||
|
BSMac Resource Report Resource Website |
BSMac (RRID:SCR_009531) | BSMac | software application, software toolkit, software resource, data processing software, image analysis software | A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results. | computational neuroscience, magnetic resonance, brain activation, connectivity, matlab, statistics, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Emory University; Georgia; USA |
PMID:22101143 PMID:17936016 |
Acknowledgement requested, BSD License, GNU Lesser General Public License, GNU General Public License | nlx_155706 | http://www.nitrc.org/projects/bsmac | SCR_009531 | BSMAC Software, Bayesian Spatial Model for Brain Activation and Connectivity, BSMac: Bayesian Spatial Model for Brain Activation and Connectivity | 2026-07-28 09:42:21 | 0 | |||||
|
INCF Neuroimaging Data Sharing Resource Report Resource Website |
INCF Neuroimaging Data Sharing (RRID:SCR_009497) | INCF Neuroimaging Data Sharing | data or information resource, narrative resource, standard specification | Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications. | community, knowledge environment, loni pipeline, magnetic resonance, nipype |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: International Neuroinformatics Coordinating Facility |
Creative Commons License | nlx_155645 | SCR_009497 | 2026-07-28 09:42:18 | 0 | ||||||||
|
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 application, software toolkit, software resource, data processing software, image analysis 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 | 2026-07-28 09:42:26 | 1 | |||||||||
|
Groupwise Image Registration Toolbox Resource Report Resource Website |
Groupwise Image Registration Toolbox (RRID:SCR_009492) | Groupwise Image Registration | software application, software resource, data processing software, registration software, image analysis software | 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 | 2026-07-28 09:42:18 | 0 | ||||||||
|
HD Neuro-Informatics Resource Report Resource Website 1+ mentions |
HD Neuro-Informatics (RRID:SCR_009493) | HDNI | data or information resource, topical portal, 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 | 2026-07-28 09:42:21 | 2 | ||||||
|
BRAINSMush Resource Report Resource Website |
BRAINSMush (RRID:SCR_009485) | BRAINSMush | software application, software resource, data processing software, segmentation software, image analysis software | Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. | analyze, application, bsd license, bsd/mit-style open source license, c++, console (text based), dicom, magnetic resonance, nifti, nrrd, segmentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155702 | http://www.nitrc.org/projects/brainsmush | SCR_009485 | 2026-07-28 09:42:26 | 0 | |||||||
|
CoCoMac-Paxinos3D viewer Resource Report Resource Website |
CoCoMac-Paxinos3D viewer (RRID:SCR_009548) | CoCoMac-Paxinos3D viewer | data visualization software, software resource, software application, data processing software | 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 | 2026-07-28 09:42:22 | 0 | ||||||
|
INVIZIAN Resource Report Resource Website 1+ mentions |
INVIZIAN (RRID:SCR_009549) | INVIZIAN | data visualization software, software resource, software application, 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 | 2026-07-28 09:42:27 | 1 | ||||||
|
Pipeline System for Octave and Matlab Resource Report Resource Website 1+ mentions |
Pipeline System for Octave and Matlab (RRID:SCR_009637) | PSOM | software application, workflow software, software resource, data processing software, software library, software toolkit | A lightweight software library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab / Octave structure. PSOM then automatically offers the following services: * Run jobs in parallel using multiple CPUs or within a distributed computing environment. * Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. * Handle job failures : successful completion of jobs is checked and failed jobs can be restarted. * Handle updates of the pipeline : change options or add jobs and let PSOM figure out what to reprocess ! | reusable library, linux, macos, matlab, microsoft, posix/unix-like, windows, workflow, octave, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Montreal; Quebec; Canada |
PMID:22493575 | MIT License | nlx_155924 | http://www.nitrc.org/projects/psom | SCR_009637 | 2026-07-28 09:42:23 | 3 | ||||||
|
PICSL Multi-Atlas Segmentation Tool Resource Report Resource Website 1+ mentions |
PICSL Multi-Atlas Segmentation Tool (RRID:SCR_009633) | PICSL Multi-Atlas Segmentation Tool | software application, software resource, data processing software, segmentation software, image analysis software | This package contains a software implementation for joint label fusion and corrective learning, which were applied in MICCAI 2012 Grand Challenge on Multi-Atlas Labeling and finished in the first place. Joint label fusion is for combining candidate segmentations produced by registering and warping multiple atlases for a target image. Corrective learning can be applied to further reduce systematic errors produced by joint label fusion. In general, corrective learning can be applied to correct systematic errors produced by other segmentation methods as well. | atlas application, segmentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155914 | SCR_009633 | 2026-07-28 09:42:20 | 2 | ||||||||
|
NIRS-SPM Resource Report Resource Website 100+ mentions |
NIRS-SPM (RRID:SCR_009630) | NIRS-SPM | software application, software resource, data analysis software, data processing software | A SPM and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. Based on the general linear model (GLM), and Sun's tube formula / Lipschitz-Killing curvature (LKC) based expected Euler characteristics, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total-hemoglobin, but also allows for super-resolution activation localization. Additional features, including a wavelet-minimum description length detrending algorithm and cerebral metabolic rate of oxygen (CMRO2) estimation without hypercapnia, were implemented in the NIRS-SPM software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | optical imaging, near-infrared spectroscopy, spm, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Korea Advanced Institute of Science and Technology; Daejeon; South Korea |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155885 | http://www.nitrc.org/projects/nirs_spm | SCR_009630 | 2026-07-28 09:42:23 | 134 |
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 PRECISE-TBI Resources search. From here you can search through a compilation of resources used by PRECISE-TBI and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that PRECISE-TBI 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 PRECISE-TBI then you can log in from here to get additional features in PRECISE-TBI 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 PRECISE-TBI 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.
