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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BEAST Resource Report Resource Website 5000+ mentions |
BEAST (RRID:SCR_010228) | sequence analysis software, data processing software, software repository, data analysis software, software application, software resource | A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. | bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: TempEst is related to: BEAST2 is related to: PhyDyn has parent organization: University of Edinburgh; Scotland; United Kingdom |
DOI:10.1186/1471-2148-7-214 | nlx_156859, OMICS_04233, biotools:beast, SCR_015988 | http://www.nitrc.org/projects/beast-library https://bio.tools/beast https://sources.debian.org/src/beast-mcmc/ |
http://beast.bio.ed.ac.uk/Main_Page | SCR_010228 | BEaST Segmentation Library, Beast Software | 2026-02-14 02:01:55 | 6460 | ||||||
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BioSig: An Imaging Bioinformatics System for Phenotypic Analysis Resource Report Resource Website 100+ mentions |
BioSig: An Imaging Bioinformatics System for Phenotypic Analysis (RRID:SCR_008428) | BioSig | data processing software, software library, software toolkit, software application, image processing software, software resource | Software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events. | application, autocorrelation, bsd, c, c++, connectivity analysis, correlation, cross-correlation, directed transfer analysis, discriminant analysis, domain independent, eeg, meg, electrocorticography, end event related potential, format conversion, german, gnome, granger causality, information theory, kde, linux, matlab, microsoft, multivariate analysis, partial directed coherence, posix/unix-like, python, regression, spectral analysis, statistical operation, temporal transformation, time domain analysis, win32 (ms windows), windows, electrocorticogram, electrocardiogram, electrooculogram, electromyogram, respiration, signal, processing, biosignal |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: Lawrence Berkeley National Laboratory |
DOI:10.1109/MC.2008.407 | Free, Available for download, Freely available | nif-0000-30190 | http://www.nitrc.org/projects/biosig https://sources.debian.org/src/biosig-tools/ |
SCR_008428 | 2026-02-14 02:01:42 | 158 | ||||||
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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 | 2026-02-14 02:02:34 | 0 | |||||||||
|
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 | 2026-02-14 02:02:34 | 5 | ||||||||
|
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 | 2026-02-14 02:02:56 | 0 | |||||||||
|
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 | 2026-02-14 02:02:53 | 39 | ||||||||
|
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 | 2026-02-14 02:02:37 | 141 | |||||||||
|
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 | 2026-02-14 02:02:37 | 1 | |||||||||
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Generation R Pediatric MRI Resources Resource Report Resource Website 10+ mentions |
Generation R Pediatric MRI Resources (RRID:SCR_014114) | data or information resource, image collection | An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication. | image collection, mri, children, ti weighted | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | SCR_014114 | 2026-02-14 02:02:53 | 15 | |||||||||||
|
Advanced Connectivity Analysis (ACA) Resource Report Resource Website 1+ mentions |
Advanced Connectivity Analysis (ACA) (RRID:SCR_014195) | ACA | software resource, data processing software, data acquisition software, software application | A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables. | data mining, data acquisition software, seed based analysis, brain behavior analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available to the research community | SCR_014195 | Advanced Connectivity Analysis (ACA): a large scale functional connectivity data mining environment, Advanced Connectivity Analysis | 2026-02-14 02:02:54 | 1 | ||||||||
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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 | 2026-02-14 02:02:37 | 0 | ||||||||||
|
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 | 2026-02-14 02:02:34 | 0 | ||||||||
|
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 | 2026-02-14 02:02:35 | 0 | |||||||
|
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 | 2026-02-14 02:02:38 | 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 | 2026-02-14 02:02:35 | 13 | |||||||||
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OpenViBE Resource Report Resource Website 50+ mentions |
OpenViBE (RRID:SCR_014156) | data visualization software, data processing software, data acquisition software, software toolkit, software application, software resource | A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time. | software toolkit, multi platform, brain computer interface, real time | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | http://openvibe.inria.fr | SCR_014156 | 2026-02-14 02:02:35 | 97 | |||||||||
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Northwestern University Schizophrenia Data and Software Tool (NUSDAST) Resource Report Resource Website |
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) | NUSDAT | data or information resource, image collection, database | A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data. | database, neuroimaging, clinical, cognitive, genetic, schizophrenia, longitudinal |
uses: CAWorks is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Northwestern University; Illinois; USA |
Schizophrenia | NIMH 1R01 MH084803; NIMH 1U01 MH097435; NIMH P50 MH071616; NIMH R01 MH056584; NCRR P41 RR15241; NIGMS U24 GM104203; NIH Bio-Informatics Research Network Coordinating Center |
Available to the research community | SCR_014153 | Northwestern University Schizophrenia Data and Software Tool | 2026-02-14 02:02:57 | 0 | ||||||
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OpenWalnut Resource Report Resource Website |
OpenWalnut (RRID:SCR_014157) | data visualization software, software resource, data processing software, software application | Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows. | open source, data visualization software, brain data, medical tool |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian |
Free, Available for download, Freely available | http://www.openwalnut.org https://sources.debian.org/src/openwalnut-qt4/ |
SCR_014157 | 2026-02-14 02:02:53 | 0 | |||||||||
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Orientation Distribution Function in Constant Solid Angle (CSA-ODF) Resource Report Resource Website |
Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (RRID:SCR_014158) | CSA ODF | data visualization software, data processing software, software toolkit, software application, software resource | A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI. | matlab, toolbox, imaging orientation, diffusion weighted mri, image reconstruction, modeling |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
Available to the research community | SCR_014158 | Orientation Distribution Function in Constant Solid Angle | 2026-02-14 02:02:37 | 0 | ||||||||
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NiiStat Resource Report Resource Website 50+ mentions |
NiiStat (RRID:SCR_014152) | data processing software, data analysis software, source code, software application, software resource | A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data. | matlab script, source code, data analysis, neuroimaging data, clinical population |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Medical University of South Carolina; South Carolina; USA |
Available to the research community | http://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage | SCR_014152 | 2026-02-14 02:02:37 | 77 |
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