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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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User Friendly Functional Connectivity - UF²C Resource Report Resource Website 1+ mentions |
User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) | UF²C | data processing software, data analysis software, software toolkit, software application, software resource, image analysis software | Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters. | standardize, functional, connectivity, brain, magnetic, resonance, imaging, graphical, user, interface, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MATLAB |
FAPESP | Free, Available for download, Freely available | SCR_016550 | User Friendly Functional Connectivity | 2026-02-13 10:57:50 | 1 | |||||||
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AngioCalc Cerebral Aneurysm Calculator Resource Report Resource Website 1+ mentions |
AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) | AngioCalc | data management software, software resource, software application | Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images. | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155693 | SCR_012805 | AngioCalc Cerebral and Peripheral Aneurysm Calculator, AngioCalc Cerebral Aneurysm Calculator | 2026-02-13 10:57:02 | 9 | |||||||||
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USC Multimodal Connectivity Database Resource Report Resource Website 10+ mentions |
USC Multimodal Connectivity Database (RRID:SCR_012809) | UMCD | data repository, storage service resource, data or information resource, service resource, database | Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. | fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: MGH-USC Human Connectome Project |
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease | NRSA ; NIH Blueprint for Neuroscience Research ; NIA F31AG035438-01; NIDA HHSN271200800035C |
PMID:23226127 PMID:20850551 |
The community can contribute to this resource, Some features require an account | nlx_83091 | http://www.nitrc.org/projects/umcd | http://jessebrown.webfactional.com/welcome/default/index | SCR_012809 | UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database | 2026-02-13 10:57:01 | 25 | ||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, portal, software development tool, software development environment, data or information resource, software application, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-02-13 10:57:04 | 24 | ||||
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Mean Machine Resource Report Resource Website |
Mean Machine (RRID:SCR_013103) | Mean Machine | data analysis software, software resource, data processing software, software application | This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz. | eeg, meg, electrocorticography, matlab | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License v2 | nlx_155808 | http://www.nitrc.org/projects/incf_mean-machi | SCR_013103 | 2026-02-13 10:57:03 | 0 | |||||||
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LiverSegm Resource Report Resource Website |
LiverSegm (RRID:SCR_013108) | LiverSegm | data processing software, software application, segmentation software, image processing software, software resource, image analysis software | A set of tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation. | liver segmentation, image processing software, injury segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP |
Free | nlx_155788 | SCR_013108 | 2026-02-13 10:57:03 | 0 | ||||||||
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Iterative dual-regression with sparse prior Resource Report Resource Website |
Iterative dual-regression with sparse prior (RRID:SCR_014128) | data analysis software, software resource, data processing software, software application | Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization. | data analysis software, neuronal activation, independent component analysis, ica, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Korea University; Seoul; South Korea |
PMID:22939873 | Available for download | SCR_014128 | 2026-02-13 10:57:14 | 0 | |||||||||
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L-Neuron Resource Report Resource Website 1+ mentions |
L-Neuron (RRID:SCR_014132) | software resource, simulation software, software application | A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth. | simulation softare, virtual neuron, neuronal modeling |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: George Mason University; Virginia; USA |
Available to the research community | http://krasnow1.gmu.edu/cn3/L-Neuron/home.htm | SCR_014132 | L Neuron | 2026-02-13 10:57:14 | 5 | ||||||||
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Lightweight Data Pipeline Resource Report Resource Website |
Lightweight Data Pipeline (RRID:SCR_014135) | software resource, workflow software, data processing software, software application | A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing. | workflow software, framework, processing pipeline, configurable shell script, cluster processing |
is used by: NCANDA: Data Integration Component is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIAAA U01 AA021697; NIBIB R01 EB008381 |
Available to the research community | SCR_014135 | 2026-02-13 10:57:14 | 0 | |||||||||
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CMIND PY Resource Report Resource Website |
CMIND PY (RRID:SCR_014097) | data processing software, software toolkit, software application, software resource, image analysis software | A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project. | python, toolbox, software toolkit, image analysis software, mri |
uses: FSL uses: ANTS - Advanced Normalization ToolS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Public | https://research.cchmc.org/c-mind-db/py-doc/html/ | SCR_014097 | CMIND-PY | 2026-02-13 10:57:13 | 0 | ||||||||
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NeuriteTracer Resource Report Resource Website 10+ mentions |
NeuriteTracer (RRID:SCR_014146) | software resource, data processing software, data acquisition software, software application | A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons. | plugin, data acquisition software, neurite outgrowth, fluorescence microscopy image, neuron |
is used by: ImageJ is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
PMID:17936365 | Availalble to the research community | http://fournierlab.mcgill.ca/styled-6/NeuriteTracer.html | SCR_014146 | 2026-02-13 10:57:14 | 39 | ||||||||
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NeuroElf Resource Report Resource Website 100+ mentions |
NeuroElf (RRID:SCR_014147) | data processing software, workflow software, software toolkit, software application, software resource | A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab. | matlab, software toolbox, brainvoyager |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVoyager |
Freely available | http://neuroelf.net http://neuroelf.net/wiki/doku.php |
SCR_014147 | 2026-02-13 10:57:13 | 141 | |||||||||
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ExPosition Packages Resource Report Resource Website 1+ mentions |
ExPosition Packages (RRID:SCR_014107) | data analysis software, software resource, data processing software, software application | An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition. | data analysis software, r package, multivariate analysis, singular value decomposition |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Texas at Dallas; Texas; USA |
https://cran.r-project.org/web/packages/ExPosition/index.html | SCR_014107 | CRAN Package Exposition | 2026-02-13 10:57:13 | 1 | |||||||||
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Biomag Discussion Group on Yahoo Resource Report Resource Website |
Biomag Discussion Group on Yahoo (RRID:SCR_014089) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG). | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014089 | 2026-02-13 10:57:13 | 0 | |||||||||||
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Image Synthesis Tools Resource Report Resource Website |
Image Synthesis Tools (RRID:SCR_014123) | image processing software, software resource, data processing software, software application | A collection of software tools developed for medical image synthesis of typically magnetic resonance (MR) brain images. The approaches have been used to create computed tomography (CT) images from MR input. The goal of image synthesis is to recover MR images with a desired optimal contrast for further processing by either registration or segmentation. | image synthesis, image restoration, software, mri, brain image, ct image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
Available for download | SCR_014123 | 2026-02-13 10:57:14 | 0 | ||||||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | data processing software, software toolkit, software application, software resource, image analysis software | A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. | image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University; Indiana; USA |
NLM R01 LM011360; NSF IIS-1117335 |
http://www.iu.edu/~hdbig/ | SCR_014120 | High Dimensional Brain Imaging Genomics Toolkit | 2026-02-13 10:57:14 | 0 | ||||||||
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APERTURE Resource Report Resource Website 1+ mentions |
APERTURE (RRID:SCR_014082) | data processing software, data analysis software, workflow software, software toolkit, software application, software resource | A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures. | matlab, software toolkit, workflow software, toolbox, multivariate analysis, data analysis |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
SCR_014082 | Analysis of Patterns in Electrophysiological Recordings Toolbox with Utilities for REsearch | 2026-02-13 10:57:13 | 3 | ||||||||||
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Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) Resource Report Resource Website |
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) (RRID:SCR_014178) | VERTEX | software resource, simulation software, software application | A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls. | simulation software, matlab, extracellular potential, spiking neural network model, snn model |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24863422 | Available to the research community | SCR_014178 | Virtual Electrode Recording Tool for EXtracellular potentials | 2026-02-13 10:57:15 | 0 | |||||||
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Wisconsin Cortical Thickness Analysis (CTA) Toolbox Resource Report Resource Website |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) | data processing software, data analysis software, software toolkit, software application, software resource | A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR). | matlab, software toolkit, cortical thickness signal, data analysis software |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Wisconsin Partnership Program ; NIA R01AG040396; NIA R01AG021155; NSF RI 1116584; NSF CAREER 1252725; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; NIA P30 AG010129; NIA K01 AG030514 |
http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html |
SCR_014180 | 2026-02-13 10:57:15 | 0 | |||||||||
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BraTumIA (Brain Tumor Image Analysis) Resource Report Resource Website 10+ mentions |
BraTumIA (Brain Tumor Image Analysis) (RRID:SCR_014184) | data processing software, software application, segmentation software, software resource, image analysis software | Segmentation software for multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences. Segmented tissues include Gray Matter, White Matter, Cerebrospinal Fluid, necrotic core, edema, non-enhancing tumor and enhancing tumor. | segmentation software, image analysis, brain tumor, volumetric segmentation, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Cancer Imaging Archive (TCIA) |
Free for non-commercial use only | SCR_014184 | BraTumIA | 2026-02-13 10:57:15 | 13 |
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