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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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FiberViewerLight Resource Report Resource Website 1+ mentions |
FiberViewerLight (RRID:SCR_009476) | FiberViewerLight | software application, software resource | Light version of the existing tool Fiber Viewer. It includes every clustering methods of Fiber Viewer such as : Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations. | c++, linux, microsoft, magnetic resonance, posix/unix-like | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155623 | SCR_009476 | 2026-09-19 12:58:07 | 5 | ||||||||
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MaCH-Admix Resource Report Resource Website 10+ mentions |
MaCH-Admix (RRID:SCR_009598) | software application, software resource | A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix. | genomic analysis, imaging genomics, imputation, snp, gene, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23074066 | Free, Non-commercial, Acknowledgement requested | nlx_155800, biotools:mach-admix | http://www.nitrc.org/projects/mach-admix, https://bio.tools/mach-admix | SCR_009598 | MaCH-Admix: Genotype Imputation Software | 2026-09-19 12:58:07 | 18 | ||||||
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Fiber-tracking based on Finsler distance Resource Report Resource Website 1+ mentions |
Fiber-tracking based on Finsler distance (RRID:SCR_009475) | Fiber-tracking based on Finsler distance | software application, software resource | Software provided as a sub-project in the Finsler-tractography module: http://www.nitrc.org/projects/finslertract | diffusion mr fiber tracking, fiber tracking, magnetic resonance, tractography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Finsler tractography module for Slicer |
3D Slicer License | nlx_155622 | SCR_009475 | 2026-09-19 12:58:07 | 1 | ||||||||
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False Discovery Rate Weighted Resource Report Resource Website 1+ mentions |
False Discovery Rate Weighted (RRID:SCR_009473) | False Discovery Rate Weighted | software application, software resource | Simple and efficient, this application performs the Weighted False Discovery Rate procedure of Benjamini and Hochberg (1997) to correct for multiple testing. The good think is that you can test virtually any number of p-values (even millions) obtained with any test-statistics for any data set. The bonus is that you can assign a-priori weights to give a better chance to those variables that you deem important. In practice, this procedure is powerful only with a relatively small number of p-values. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155620 | SCR_009473 | 2026-09-19 12:58:07 | 1 | |||||||||
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LDDMM Resource Report Resource Website 10+ mentions |
LDDMM (RRID:SCR_009590) | LDDMM | software application, software resource | Software application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes. As part of these efforts the Center for Imaging Science at Johns Hopkins University developed techniques to not only compare images, but also to visualize the changes and differences. For additional information please refer to: Faisal Beg, Michael Miller, Alain Trouve, and Laurent Younes. Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision, Volume 61, Issue 2; February 2005. M.I. Miller and A. Trouve and L. Younes, On the Metrics and Euler-Lagrange Equations of Computational Anatomy, Annual Review of biomedical Engineering, 4:375-405, 2002. Software developed with support from National Institutes of Health NCRR grant P41 RR15241. | analyze, c++, console (text based), linux, microsoft, magnetic resonance, posix/unix-like, shape analysis, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
nlx_155780 | http://www.nitrc.org/projects/lddmm-volume | SCR_009590 | Large Deformation Diffeomorphic Metric Mapping | 2026-09-19 12:58:07 | 31 | |||||||
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GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data Resource Report Resource Website 1+ mentions |
GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data (RRID:SCR_009581) | GMAC | software resource, software toolkit | Open-source software toolbox implemented multivariate spectral Granger Causality Analysis for studying brain connectivity using fMRI data. Available features are: fMRI data importing, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions are integrated into a graphical user interface developed in Matlab environment. Dependencies: Matlab, BIOSIG, SPM, MarsBar. | analyze, computational neuroscience, connectivity analysis, matlab, magnetic resonance, nifti, os independent, fmri, connectivity, granger causality, network analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Polytechnic University of Milan; Milan; Italy |
NIH Blueprint for Neuroscience Research | PMID:22925560 | nlx_155764 | http://www.nitrc.org/projects/gmac_2012 | http://selene.bioing.polimi.it/BBBlab/GMAC/ | SCR_009581 | Granger Multivariate Autoregressive Connectivity | 2026-09-19 12:58:07 | 1 | ||||
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BrainGraph Editor Resource Report Resource Website 1+ mentions |
BrainGraph Editor (RRID:SCR_009536) | BrainGraph Editor | software application, software resource | A JAVA application designed to create taxonomies or hierarchies in order to classify and organize information. | gnome, information resource, information specification, java, kde, ontology, os independent, visualization, win32 (ms windows), taxonomy, hierarchy, classify, organize |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
BIRN License, LONI Software License | nlx_155713 | http://www.nitrc.org/projects/braingrpheditor | SCR_009536 | 2026-09-19 12:58:07 | 3 | |||||||
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ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar, https://bio.tools/annovar | SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-09-19 12:58:08 | 6463 | |||||
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Solar Eclipse Imaging Genetics tools Resource Report Resource Website 10+ mentions |
Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) | Solar Eclipse Imaging Genetics tools | software application, software resource | Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data | c++, genetic association, genomic analysis, gifti, imaging genomics, linux, loni pipeline, macos, microsoft, nifti, posix/unix-like, snp, gene, windows, windows xp, genetics, neuroimaging, heritability, pleiotropy, quantitative trait loci, genome-wide association, gene expression, methylation, trait, structural neuroimaging, functionalneuroimaging, brain imaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Non-commercial, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552 | nlx_155966 | SCR_009645 | 2026-09-19 12:58:07 | 14 | ||||||||
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Generalized PPI Toolbox Resource Report Resource Website 50+ mentions |
Generalized PPI Toolbox (RRID:SCR_009489) | software resource, software toolkit | An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The automated toolbox can do the following: (a1) produce identical results to the current implementation in SPM (a2) use the current implementation of PPI in SPM but using the regional mean instead of the eigenvariate (a3) use a generalized form that allows a PPI for each task to be in the same model using either the regional mean of eigenvariate (b) create the model using the output of one of the (a) options and the first level design (c) estimate the model (/results directory) (d) compute the contrasts specified. | magnetic resonance, psychophysiological interaction, fmri, neuroimaging, automated toolbox, spm, fsfast | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Acknowledgement requested, Available for download | nlx_155636 | SCR_009489 | Generalized Psychophysiological Interaction Toolbox | 2026-09-19 12:58:07 | 56 | ||||||||
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dcm2nii Resource Report Resource Website 100+ mentions |
dcm2nii (RRID:SCR_014099) | software application, software resource, systems interoperability software | A tool for converting images from the complicated formats used by scanner manufacturers (DICOM, PAR/REC) to the NIfTI format used by various scientific tools. dcm2nii works for all modalities (CT, MRI, PET, SPECT) and sequence types. | image converter, nifti format, systems interoperability software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of South Carolina; South Carolina; USA |
NIDCD R01DC009571; NIDCD U01DC011739 |
Available for download | http://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage | SCR_014099 | 2026-09-19 12:58:11 | 205 | ||||||||
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iso2mesh Resource Report Resource Website 10+ mentions |
iso2mesh (RRID:SCR_013202) | iso2mesh | software application, software resource, software toolkit | A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling. | matlab, mesh generation, modeling, magnetic resonance, optical imaging, os independent, mri, computed tomography, octave |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155855 | http://www.nitrc.org/projects/iso2mesh | SCR_013202 | 2026-09-19 12:58:09 | 28 | |||||||
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GenGen Resource Report Resource Website 10+ mentions |
GenGen (RRID:SCR_013447) | GenGen | software application, software resource | A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. | genomic analysis, imaging genomics, pathway, network, snp, gene, genetics, genomics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: OpenBioinformatics.org |
Free | nlx_155766 | http://www.nitrc.org/projects/gengen | SCR_013447 | GenGen: Genetic Genomics Analysis of Complex Data | 2026-09-19 12:58:10 | 26 | ||||||
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MDR Resource Report Resource Website 10+ mentions |
MDR (RRID:SCR_013427) | MDR | software application, software resource | Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
nlx_154096 | http://www.nitrc.org/projects/mdr | SCR_013427 | Multifactor Dimensionality Reduction | 2026-09-19 12:58:10 | 39 | |||||||
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Brain Decoder Toolbox Resource Report Resource Website 1+ mentions |
Brain Decoder Toolbox (RRID:SCR_013150) | BDTB | software application, software resource | Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent. | analyze, japanese, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
PMID:15852014 | GNU General Public Licence | nlx_155709 | http://www.nitrc.org/projects/bdtb | SCR_013150 | BrainDecoderToolbox | 2026-09-19 12:58:09 | 2 | |||||
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DTI denoising Resource Report Resource Website |
DTI denoising (RRID:SCR_014102) | software resource, software toolkit | A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures. | software toolkit, matlab package, denoise, filter, dwi, image redundancy, imager sparsity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Bordeaux Segalen University; Bordeaux; France has parent organization: Polytechnic University of Valencia; Valencia; Spain |
Free for non-commercial use | SCR_014102 | DWIdenoisingPackage, DWI Denoising Package | 2026-09-19 12:58:11 | 0 | |||||||||
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Kitware Resource Report Resource Website 10+ mentions |
Kitware (RRID:SCR_013989) | service resource, software repository, software resource | A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training. | software repository, open source, visualization, computer vision, medical imaging, data publishing, quality software process solutions |
is listed by: Connected Researchers is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VTK CISG Registration Toolkit is related to: Connected Researchers is parent organization of: Midas Platform is parent organization of: ParaView is parent organization of: VolView is parent organization of: VTK |
PASCAL network of excellence ; Max-Planck Society ; Fraunhofer Society |
Open source | SCR_013989 | 2026-09-19 12:58:11 | 12 | |||||||||
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SFMProject Resource Report Resource Website |
SFMProject (RRID:SCR_014166) | software repository, software resource | Structure from motion algorithms repository. Common interface for various sfm algorithms. | motion algorithm, repository, sfm algorithm | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014166 | 2026-09-19 12:58:11 | 0 | ||||||||||
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BrainBox Resource Report Resource Website 10+ mentions |
BrainBox (RRID:SCR_014750) | software application, software resource | Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community. | web application, data visualization software, mri, dataset, visualization, segment, nifti, collaboration |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) works with: MetaSearch is hosted by: Open Neuroimaging Laboratory is hosted by: GitHub |
Public | https://www.nitrc.org/projects/brainbox | SCR_014750 | 2026-09-19 12:58:12 | 11 | |||||||||
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EPILEPSIE database Resource Report Resource Website 1+ mentions |
EPILEPSIE database (RRID:SCR_003179) | data or information resource, database | A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data. | seizure, electroencephalography, mri, eeg recording, metadata, intracranial, surface, time series analyses, brain activity, brain, clinical, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
Epilepsy | Excellence Initiative of the German Federal and State Governments ; European Union 211713; BMBF 01GQ0420; German Science Foundation Ti 315/4-2 |
PMID:22738131 | Free, Freely available | nlx_156892 | http://www.nitrc.org/projects/epilepsiaedb http://epilepsy-database.eu/project/ http://www.epilepsiae.eu http://epilepsy-database.eu | SCR_003179 | EPILEPSIAE Project Database, European Epilepsy Database | 2026-09-19 12:56:39 | 3 |
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