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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BrainGraph Editor Resource Report Resource Website 1+ mentions |
BrainGraph Editor (RRID:SCR_009536) | BrainGraph Editor | software resource, software application | 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 | 2026-02-14 02:07:08 | 3 | |||||||
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ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software resource, software application | 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 | 2026-02-14 02:07:21 | 5946 | |||||
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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 resource, software application | 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 | 2026-02-14 02:07:21 | 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 | 2026-02-14 02:07:08 | 51 | ||||||||
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dcm2nii Resource Report Resource Website 100+ mentions |
dcm2nii (RRID:SCR_014099) | systems interoperability software, software resource, software application | 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 | 2026-02-14 02:06:56 | 191 | ||||||||
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iso2mesh Resource Report Resource Website 10+ mentions |
iso2mesh (RRID:SCR_013202) | iso2mesh | software resource, software toolkit, software application | 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 | 2026-02-14 02:07:22 | 25 | |||||||
|
GenGen Resource Report Resource Website 10+ mentions |
GenGen (RRID:SCR_013447) | GenGen | software resource, software application | 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 | 2026-02-14 02:07:12 | 25 | ||||||
|
MDR Resource Report Resource Website 10+ mentions |
MDR (RRID:SCR_013427) | MDR | software resource, software application | 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 | 2026-02-14 02:07:23 | 38 | |||||||
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Brain Decoder Toolbox Resource Report Resource Website 1+ mentions |
Brain Decoder Toolbox (RRID:SCR_013150) | BDTB | software resource, software application | 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 | 2026-02-14 02:07:17 | 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 | 2026-02-14 02:07:14 | 0 | |||||||||
|
Kitware Resource Report Resource Website 10+ mentions |
Kitware (RRID:SCR_013989) | software resource, service resource, software repository | 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 | 2026-02-14 02:06:56 | 12 | |||||||||
|
BrainBox Resource Report Resource Website 10+ mentions |
BrainBox (RRID:SCR_014750) | software resource, software application | 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 | 2026-02-14 02:06:57 | 11 | |||||||||
|
SFMProject Resource Report Resource Website |
SFMProject (RRID:SCR_014166) | software resource, software repository | 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 | 2026-02-14 02:07:19 | 0 | ||||||||||
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Epilepsy T1 and Hippocampal Segmentation Datasets Resource Report Resource Website |
Epilepsy T1 and Hippocampal Segmentation Datasets (RRID:SCR_014926) | data or information resource, data set | Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site. | hippocampus, t1, dataset, skull stripped, mri, segmented hippocampus, epilepsy, temporal lobe epilepsy, tle | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_014926 | 2026-02-14 02:07:58 | 0 | ||||||||||
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Stark Cross-Sectional Aging Resource Report Resource Website |
Stark Cross-Sectional Aging (RRID:SCR_014171) | data or information resource, data set | Behavioral and imaging data from about 120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes traditional neuropsycholgical measures, hippocampal-specific behavioral measures, whole-brain DTI, high-resolution DTI of the medial temporal lobes, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields. | data set, aging, hippocampus, behavioral, dti, mri, image |
uses: Neuroimaging Informatics Technology Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
NIA R01 AG034613 | Available to the research community | SCR_014171 | 2026-02-14 02:07:50 | 0 | |||||||||
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Papaya Resource Report Resource Website 1+ mentions |
Papaya (RRID:SCR_014188) | software resource, source code | A pure JavaScript medical research image viewer, compatible across a range of popular web browsers. The orthogonal viewer supports NIFTI and DICOM files, overlays and atlas labels. It requires Firefox (7+), Chrome (7+), Safari (6+), MobileSafari (iOS 6+), or IE (10+). | source code, javascript, medical research, image viewer | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | https://github.com/rii-mango/Papaya/ | SCR_014188 | 2026-02-14 02:07:56 | 5 | |||||||||
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Efficient Permutation Testing Resource Report Resource Website |
Efficient Permutation Testing (RRID:SCR_014104) | software resource, source code | A Matlab implementation for efficient permutation testing by using matrix completion. | permutation, nueroimaging, source code, fast, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Wisconsin Partnership Fund ; NIA R01 AG040396; NSF CAREER 1252725; NSF RI 1116584; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; Veterans Administration Merit Review I01CX000165 |
Available for download, Acknowledgement requested | http://pages.cs.wisc.edu/~vamsi/pt_fast.html | SCR_014104 | Speeding Up Permutation Testing in Neuroimaging | 2026-02-14 02:08:23 | 0 | |||||||
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YMDTI: Diffusion Tensor Images of Healthy Young Males Resource Report Resource Website |
YMDTI: Diffusion Tensor Images of Healthy Young Males (RRID:SCR_014183) | YMDTI | data or information resource, data set | A dataset which contains diffusion tensor images of 93 healthy, young male subjects. | data set, diffusion tensor image, young male subject | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014183 | Diffusion Tensor Images of Healthy Young Males | 2026-02-14 02:08:23 | 0 | ||||||||
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Statistical non-Parametric Mapping Resource Report Resource Website 50+ mentions |
Statistical non-Parametric Mapping (RRID:SCR_002092) | SnPM | data processing software, software resource, software toolkit, software application | A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM. | analyze, linear, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, regression, statistical operation, sunos/solaris, windows, statistical parametric mapping, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: SPM has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Warwick; Coventry; United Kingdom |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00342 | http://www.nitrc.org/projects/snpm | SCR_002092 | SnPM: Statistical nonParametric Mapping, SnPM - Statistical NonParametric Mapping - A toolbox for SPM, Statistical nonParametric Mapping | 2026-02-14 02:05:25 | 95 | |||||
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Wavelet-based Image Fusion Resource Report Resource Website 1+ mentions |
Wavelet-based Image Fusion (RRID:SCR_002007) | Wavelet-based Image Fusion | data processing software, software resource, software toolkit, software application | Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012). | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:21761448 | Free, Available for download, Freely available | nlx_156018 | SCR_002007 | 2026-02-14 02:05:21 | 2 |
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