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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ISRNA Resource Report Resource Website 1+ mentions |
ISRNA (RRID:SCR_009565) | ISRNA | software resource | An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:24300438 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00360 | SCR_009565 | Integrative Short Reads NAvigator | 2026-08-29 11:23:35 | 3 | |||||||
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DTI-Reg Resource Report Resource Website |
DTI-Reg (RRID:SCR_009560) | DTI-Reg | data processing software, image analysis software, registration software, software application, software resource | An open-source C++ application that performs pair-wise DTI registration, using scalar FA map to drive the registration. Individual steps of the pair-wise registration pipeline are performed via external applications - some of them being 3D Slicer modules. Starting with two input DTI images, scalar FA maps are generated via dtiprocess. Registration is then performed between these FA maps, via BRAINSFit/BRAINSDemonWarp or ANTS -Advanced Normalization Tools-, which provide different registration schemes: rigid, affine, BSpline, diffeomorphic, logDemons. The final deformation is then applied to the source DTI image via ResampleDTI. | analyze, c++, magnetic resonance, nrrd, os independent, registration, resampling, spatial transformation, workflow | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155740 | http://www.nitrc.org/projects/dtireg | SCR_009560 | 2026-08-29 11:23:34 | 0 | |||||||
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shortran Resource Report Resource Website |
shortran (RRID:SCR_009636) | shortran | software resource | A pipeline for small RNA-seq data analysis. | is listed by: OMICtools | PMID:22914220 | Free | OMICS_00368 | SCR_009636 | 2026-08-29 11:23:22 | 0 | ||||||||
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Pipeline System for Octave and Matlab Resource Report Resource Website 1+ mentions |
Pipeline System for Octave and Matlab (RRID:SCR_009637) | PSOM | data processing software, software application, software library, software resource, software toolkit, workflow software | 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 | 2026-08-29 11:23:36 | 3 | ||||||
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NordicNeuroLab Resource Report Resource Website 50+ mentions |
NordicNeuroLab (RRID:SCR_009632) | NNL | commercial organization | From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike. | analyze, ascii, dicom, diffusion mr fiber tracking, experiment control, eye tracking, fiber tracking, haemodynamic response, hardware, microsoft, magnetic resonance, nifti, perfusion, physiological recording, scanner, stimulus presentation, temporal curve fitting, temporal transformation, tractography, windows, windows vista, windows xp, fmri, post-processing, visualization, bold, diffusion, dti, perfusion, dce, audio stimulation, visual stimulation, eye tracking, patient response, clinical, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial | nlx_155905 | http://www.nitrc.org/projects/nnl | SCR_009632 | 2026-08-29 11:23:22 | 57 | |||||||
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PICSL Multi-Atlas Segmentation Tool Resource Report Resource Website 1+ mentions |
PICSL Multi-Atlas Segmentation Tool (RRID:SCR_009633) | PICSL Multi-Atlas Segmentation Tool | data processing software, image analysis software, segmentation software, software application, software resource | 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 | 2026-08-29 11:23:36 | 2 | ||||||||
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NIRS-SPM Resource Report Resource Website 100+ mentions |
NIRS-SPM (RRID:SCR_009630) | NIRS-SPM | data analysis software, data processing software, software application, software resource | 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 | 2026-08-29 11:23:36 | 137 | |||||||
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NITRC Community Resource Report Resource Website |
NITRC Community (RRID:SCR_009631) | NITRC Community | community building portal, data or information resource, portal | NITRC-wide community facilities: Forums, Wiki, Tracker, and News. | forum, event, news, funding, wiki, document, job resource |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
nlx_155888 | SCR_009631 | 2026-08-29 11:23:38 | 0 | |||||||||
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Lipsia Resource Report Resource Website 10+ mentions |
Lipsia (RRID:SCR_009595) | Lipsia | data processing software, image analysis software, image processing software, software application, software resource | 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 | 2026-08-29 11:23:35 | 41 | |||||
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Lumina LP- 400 Response System Resource Report Resource Website |
Lumina LP- 400 Response System (RRID:SCR_009596) | Lumina LP-400 | instrument resource | A reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields. | experiment control, hardware, magnetic resonance, response monitoring, fmri, clinical, research, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155789 | http://www.nitrc.org/projects/lumina | http://www.cedrus.com/ordering/mri/usa.htm | SCR_009596 | Lumina fMRI Input Device, Lumina LP-400 System for fMRI, Lumina fMRI Response Pad | 2026-08-29 11:23:38 | 0 | ||||||
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LIMO EEG Resource Report Resource Website 10+ mentions |
LIMO EEG (RRID:SCR_009592) | LIMO EEG | data processing software, image analysis software, image processing software, software application, software resource, 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 | 2026-08-29 11:23:21 | 11 | |||||||
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Multi-fiber Reconstruction from DW-MRI Resource Report Resource Website |
Multi-fiber Reconstruction from DW-MRI (RRID:SCR_009509) | Multi-fiber Reconstruction from DW-MRI | software resource | This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program, namely, Mixture of Wisharts (MOW), Diffusion Orientation Transform (DOT) and Q-ball Imaging (QBI). This program is mainly developed and maintained by Bing Jian, as part of his Ph.D. research, supervised by Prof. Baba Vemuri. Please note that the source code of this program is hosted at Google Code, see the Source Code link on the left. | reusable library, console (text based), diffusion mr fiber tracking, fiber tracking, magnetic resonance, os independent, python, tractography, reconstruction, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
GNU General Public License | nlx_155669 | SCR_009509 | 2026-08-29 11:23:33 | 0 | ||||||||
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MASIMatlab Resource Report Resource Website 1+ mentions |
MASIMatlab (RRID:SCR_009506) | MASIMatlab | software resource | This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling. | magnetic resonance, matlab, population characterization, mri, dti, smri, qmri, shape modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
nlx_155655 | SCR_009506 | 2026-08-29 11:23:19 | 4 | |||||||||
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iView X MRI-LR - Eye Tracking for fMRI Resource Report Resource Website 1+ mentions |
iView X MRI-LR - Eye Tracking for fMRI (RRID:SCR_009627) | iView X MRI-LR | software resource | A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output | magnetic resonance, fmri, meg, eye, eye tracking, mri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commerical | nlx_155853 | http://www.nitrc.org/projects/iviewx_mri-lr | SCR_009627 | 2026-08-29 11:23:38 | 3 | |||||||
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MASI Label Fusion Resource Report Resource Website 1+ mentions |
MASI Label Fusion (RRID:SCR_009505) | MASI Label Fusion | software resource | Tool that provides a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE. In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
GNU Lesser General Public License | nlx_155654 | SCR_009505 | 2026-08-29 11:23:37 | 3 | ||||||||
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iTools Resource Report Resource Website 50+ mentions |
iTools (RRID:SCR_009626) | iTools | data access protocol, data or information resource, data repository, database, service resource, software repository, software resource, storage service resource, web service | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools, http://www.loni.usc.edu/research/software | http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-08-29 11:23:36 | 53 | |||
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DFCI Biospecimen Repository Core Facility Resource Report Resource Website |
DFCI Biospecimen Repository Core Facility (RRID:SCR_009747) | access service resource, biospecimen repository, core facility, material storage repository, service resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core facility that provides the following services: Storage services for -80 degrees C and -190 degrees C in secure facility. The Biospecimen Repository provides long-term storage of clinical and research material in -80 degrees C and liquid nitrogen freezers located at Dana Farber''s Harbor Campus. Transportation of samples to and from Harbor Campus is provided by the facility for a small fee. Competitive prices are available on per box or per freezer basis in both segregated or non-segregated environments. |
material storage |
is listed by: Eagle I has parent organization: Dana-Farber Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156208 | http://research4.dfci.harvard.edu/issues/DryDock, http://www.dana-farber.org/Research/Core-Facilities.aspx#biospecimen | SCR_009747 | 2026-08-29 11:23:23 | 0 | ||||||||
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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) | data processing software, image processing software, software application, software resource, 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) |
Junta de Castilla y Leon ; Ministerio de Ciencia y Educacion |
Free, Available for download, Freely available | nlx_155649, SCR_014129 | SCR_009502 | Joint Anisotropic LMMSE Filter for Stationary Rici | 2026-08-29 11:23:37 | 1 | |||||||
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fanDTasia Java Applet: DT-MRI Processing Resource Report Resource Website 1+ mentions |
fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) | fdt | data processing software, image processing software, software application, software resource | A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser. | magnetic resonance, dti, diffusion-weighted mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NIBIB EB007082; NINDS NS066340 |
Non-Commercial Software License Agreement, Https://www.nitrc.org/include/glossary.php#589, Non-commercial | nlx_155849 | http://www.nitrc.org/projects/fandtasia | SCR_009624 | FanDTasia | 2026-08-29 11:23:22 | 2 | |||||
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JIP Analysis Toolkit Resource Report Resource Website 10+ mentions |
JIP Analysis Toolkit (RRID:SCR_009588) | JIP Toolkit | data processing software, image analysis software, software application, software resource, software toolkit | 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 | 2026-08-29 11:23:35 | 29 |
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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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