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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | data processing software, software application, software resource, workflow software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-09-19 12:49:35 | 11 | |||
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Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | data or information resource, portal, software resource, topical portal | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-09-19 12:49:35 | 84 | |||||
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VectorValuedHistogramNormalizer Resource Report Resource Website |
VectorValuedHistogramNormalizer (RRID:SCR_000082) | VectorValuedHistogramNormalizer | software resource | Software tool for MRI intensity standardization by aligning histograms of higher dimensions. The methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf are implemented as and ITK filter. | magnetic resonance, mri, standardization, histogram, intensity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: INCF Software Center has parent organization: University of Erlangen-Nuremberg; Bavaria; Germany |
Free, Freely Avaliable | nlx_156014 | SCR_000082 | 2026-09-19 12:49:15 | 0 | ||||||||
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Dipy Resource Report Resource Website 10+ mentions |
Dipy (RRID:SCR_000029) | DIPY | data analysis software, data processing software, software application, software resource, software toolkit | Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data. | MRI, magnetic resonance, diffusion data analysis, diffusion MRI data, diffusion MRI data analysis, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Neuroimaging in Python has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:24600385 | Free, Available for download, Freely available | nlx_155745 | https://sources.debian.org/src/python-dipy/, http://www.nitrc.org/projects/dipy, http://elef.soic.indiana.edu/, https://github.com/nipy/dipy_web, | http://nipy.org/dipy/ | SCR_000029 | Diffusion Imaging In Python, NIPY Diffusion Imaging Analysis | 2026-09-19 12:49:14 | 16 | ||||
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Clinical Toolbox for SPM Resource Report Resource Website 10+ mentions |
Clinical Toolbox for SPM (RRID:SCR_014096) | data management software, software application, software resource, software toolbox | A clinical toolbox useful for normalizing data from individuals with brain injury and/or modalities popular in the clinical environment (CT). It supports either enantiomorphic or lesion-masked normalization. It can be either scripted or used with SPM's simple graphical interface. | software toolkit, clinical toolbox, normalization, data management software, human brain, brain injury, spm |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: SPM has parent organization: University of South Carolina; South Carolina; USA |
Available for download | http://www.mccauslandcenter.sc.edu/CRNL/clinical-toolbox | SCR_014096 | 2026-09-19 12:52:51 | 10 | |||||||||
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Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation Resource Report Resource Website |
Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation (RRID:SCR_014108) | data processing software, data visualization software, software application, software resource | A tool which offers a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units (GPUs). The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data. | data visualization software, myelin map, t2 data, parallel computation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of British Columbia; British Columbia; Canada |
MS/MRI Research Group at the University of British Columbia ; Natural Sciences and Engineering Research Council of Canada ; Milan and Maureen Ilich Foundation |
Available for download | SCR_014108 | 2026-09-19 12:52:52 | 0 | |||||||||
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Forward: Accurate finite element electromagnetic head models Resource Report Resource Website 10+ mentions |
Forward: Accurate finite element electromagnetic head models (RRID:SCR_014109) | simulation software, software application, software resource | A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included. | model, simulation software, electromagnetic head model, eeg forward modeling, mapping |
uses: Nipype is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Liege; Wallonia; Belgium |
Belgian National Fund for Scientific Research ; Marie Curie Initial Training Network in Neurophysics PITN-GA-2009-238593 |
SCR_014109 | Forward | 2026-09-19 12:52:52 | 13 | |||||||||
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ERPwavelab Resource Report Resource Website 1+ mentions |
ERPwavelab (RRID:SCR_014106) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain. | software toolbox, data analysis, data visualization, eeg data, meg data, plugin, time frequency domain, fourier time domain analysis, temporal wavelet analysis |
is used by: EEGLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Technical University of Denmark; Lyngby; Denmark |
Open source | http://www.erpwavelab.org | SCR_014106 | 2026-09-19 12:52:51 | 9 | |||||||||
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Functional Connectivity Analysis Tool for near-infrared spectroscopy data Resource Report Resource Website 1+ mentions |
Functional Connectivity Analysis Tool for near-infrared spectroscopy data (RRID:SCR_014111) | FC-NIRS | data analysis software, data processing software, network analysis software, software application, software resource | A functional connectivity analysis tool for near-infrared spectroscopy data. Its functions include preprocessing, quality control, FC calculation and network analysis. | network analysis, data processing software, functional connectivity analysis, near infrared spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: GRETNA has parent organization: Beijing Normal University; Beijing; China |
Natural Science Foundation of China 81201122; Natural Science Foundation of China 81571755; Fundamental Research Funds for the Central Universities 2012LYB06; Beijing Natural Science Foundation Z111107067311036; Specialized Research Fund for the Doctoral Program of Higher Education ; Open Research Fund of the State Key Laboratory of Cognitive Neuroscience and Learning |
Available for download | SCR_014111 | 2026-09-19 12:52:52 | 1 | ||||||||
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freesurfR Resource Report Resource Website |
freesurfR (RRID:SCR_014110) | data analysis software, data processing software, software application, software resource, software toolkit | A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2. | data analysis software, software package, group analysis, freesurfer, surface data, r linear model |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Available for download | SCR_014110 | 2026-09-19 12:52:52 | 0 | ||||||||||
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Graph Theory GLM (GTG) MATLAB Toolbox Resource Report Resource Website 1+ mentions |
Graph Theory GLM (GTG) MATLAB Toolbox (RRID:SCR_014075) | GTG | data analysis software, data processing software, software application, software resource | A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times. | MATLAB, Connectivity Analysis, fMRI, data analysis software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Boston University; Massachusetts; USA |
http://sites.bu.edu/metalab/tools/ | SCR_014075 | Graph Theory GLM, GTG MATLAB Toolbox | 2026-09-19 12:52:51 | 6 | ||||||||
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bic-mni-models Resource Report Resource Website 10+ mentions |
bic-mni-models (RRID:SCR_014087) | data or information resource, image collection | Anatomical brain template library which includes models from ICBM 2009 template.Number of unbiased non-linear averages of MNI152 database have been generated that combines attractions of both high-spatial resolution and signal-to-noise while not being subject to vagaries of any single brain. Procedure involved multiple iterations of process where, at each iteration, individual native MRIs were non-linearly fitted to the average template from previous iteration, beginning with MNI152 linear template. | brain template, anatomical brain library, image collection, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ICBM 152 Nonlinear atlases version 2009 has parent organization: McGill University; Montreal; Canada |
SCR_014087 | 2026-09-19 12:52:51 | 44 | |||||||||||
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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 | 2026-09-19 12:52:51 | 0 | ||||||||
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Laplace Beltrami Filter on QuadEdge Meshes Resource Report Resource Website |
Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) | data acquisition software, data processing software, software application, software resource | A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface. | data acquisition software, filter, laplace beltrami, surface harmonic |
is used by: Insight Segmentation and Registration Toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIBIB R01-EB008171-01A1; NCRR P41-RR015241 |
Available to the research community | SCR_014133 | Laplace-Beltrami Filter on QuadEdge Meshes | 2026-09-19 12:52:52 | 0 | ||||||||
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libSBML Resource Report Resource Website 10+ mentions |
libSBML (RRID:SCR_014134) | catalog, data or information resource, database | A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications. | markup language, systems biology, programming library, catalog | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Open source | http://sourceforge.net/p/sbml/code/HEAD/tree/ | SCR_014134 | Systems Biology Markup Language Library, Library for Systems Biology Markup Language | 2026-09-19 12:52:52 | 40 | ||||||||
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KWScene: MRML-based Atlas and Scene Builder/Reader/Writer Resource Report Resource Website |
KWScene: MRML-based Atlas and Scene Builder/Reader/Writer (RRID:SCR_014131) | data management software, data processing software, software application, software resource | ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView. | data management software, data processing, visualization, medical imaging, plugin | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | http://www.vtk.org/Wiki/KWScene, https://www.kitware.com/svn/KWPublic/trunk/KWScene/ | SCR_014131 | KWScene, KWScene: MRML-based Atlas and Scene Builder/Reader/Writer collaboration with Kitware | 2026-09-19 12:52:52 | 0 | ||||||||
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MARS (Multi-Atlas Robust Segmentation) Resource Report Resource Website 1+ mentions |
MARS (Multi-Atlas Robust Segmentation) (RRID:SCR_014137) | data processing software, image analysis software, segmentation software, software application, software resource | Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods. | segmentation software, anatomical structure, label, multi atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:24315359 | Available to the research community | SCR_014137 | 2026-09-19 12:52:52 | 5 | |||||||||
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minc-toolkit Resource Report Resource Website 1+ mentions |
minc-toolkit (RRID:SCR_014138) | data processing software, image processing software, software application, software resource, software toolkit | A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp. | image processing, software package |
uses: minc-toolkit-testsuite is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Available to the research community | http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit, https://github.com/BIC-MNI/minc-toolkit | SCR_014138 | MINC Tool Kit | 2026-09-19 12:52:52 | 9 | ||||||||
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Neoseg Resource Report Resource Website 1+ mentions |
Neoseg (RRID:SCR_014144) | data processing software, image analysis software, segmentation software, software application, software resource | A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior. | segmentation software, automatic segmentation, neonatal brain mri |
is used by: NeoSegPipeline is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Available to the research community | https://github.com/NIRALUser/neoseg/tree/master | SCR_014144 | 2026-09-19 12:52:52 | 2 | |||||||||
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NeoSegPipeline Resource Report Resource Website |
NeoSegPipeline (RRID:SCR_014145) | data processing software, image analysis software, segmentation software, software application, software resource | This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results. | segmentation software, atlas, brain mri, diffusion image |
uses: Neoseg uses: NIRAL Utilities is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: UNC Human Brain Atlas |
Available to the research community | https://github.com/marie-cherel2013/NeosegPipeline/tree/master/NeosegPipeline | SCR_014145 | 2026-09-19 12:52:52 | 0 |
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