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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 | 2026-08-04 09:42:23 | 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 | 2026-08-04 09:42:24 | 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 | 2026-08-04 09:42:23 | 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 | 2026-08-04 09:42:23 | 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 | 2026-08-04 09:42:24 | 30 | |||||||
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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 | 2026-08-04 09:43:09 | 2 | |||||
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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 | 2026-08-04 09:42:25 | 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 | 2026-08-04 09:43:05 | 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 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 | 2026-08-04 09:42:26 | 14 | ||||||||
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dcm2nii Resource Report Resource Website 100+ mentions |
dcm2nii (RRID:SCR_014099) | systems interoperability software, software application, software resource | 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 | 2026-08-04 09:43:20 | 191 | ||||||||
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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 | 2026-08-04 09:43:13 | 25 | ||||||
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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 | 2026-08-04 09:43:31 | 11 | |||||||||
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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 | 2026-08-04 09:43:12 | 38 | |||||||
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Kitware Resource Report Resource Website 10+ mentions |
Kitware (RRID:SCR_013989) | service resource, software 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 | 2026-08-04 09:43:18 | 12 | |||||||||
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Morphometry BIRN Resource Report Resource Website |
Morphometry BIRN (RRID:SCR_000155) | MBIRN | data set, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th,2023. Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains. | morphometry, mri, neuroinformatics, subcortical, dicom, magnetic resonance, nifti, quantification, segmentation, visualization, workflow, image collection, structural mri, male, female, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: XNAT Central has parent organization: Biomedical Informatics Research Network is parent organization of: Gradient Non-linearity Distortion Correction is parent organization of: Gradient Non-linearity Distortion Correction |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00069 | http://www.nitrc.org/projects/mbirn | SCR_000155 | Morphometry BIRN Multi-site Multi-session Structural MRI Data, Brain Morphometry Testbed, Morphometry Testbed, mBIRN_calib, mbirn calibration | 2026-08-04 09:40:04 | 0 | ||||||
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MINC Example files Resource Report Resource Website |
MINC Example files (RRID:SCR_000859) | MINC Example files | data set, data or information resource | A reference MINC set of files that currently includes human head images only of standard modalities. The goal is to build a well curated collection of files that demonstrate the capabilities of MINC | image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MINC has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155660 | SCR_000859 | 2026-08-04 09:40:15 | 0 | ||||||||
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Internet Brain Segmentation Repository Resource Report Resource Website 10+ mentions |
Internet Brain Segmentation Repository (RRID:SCR_001994) | IBSR | data set, data or information resource | Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results. | 3d model, anatomy, brainstem, cerebellum, cortex, gray matter, imaging, morphology, mri, segmentation, volume, white matter, adult human, male, child, image collection, application, magnetic resonance, os independent, php, quality metrics, segmentation, test data, web service |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
Normal, Tumor | NINDS 1 R01 NS34189-01 | Free, Available for download, Freely available | nif-0000-00032 | http://www.cma.mgh.harvard.edu/ibsr/ | SCR_001994 | 2026-08-04 09:40:31 | 24 | |||||
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Rosetta Bit Resource Report Resource Website 1+ mentions |
Rosetta Bit (RRID:SCR_001906) | Rosetta Bit | data set, data or information resource | Public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data. | computed tomography, imaging genomics, magnetic resonance, optical imaging, format conversion, dicom, nifti, dicom, par/rec | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155947 | SCR_001906 | 2026-08-04 09:40:30 | 1 | ||||||||
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MCIC Resource Report Resource Website 10+ mentions |
MCIC (RRID:SCR_002310) | MCIC | data set, data or information resource | Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and gender and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). This data repository will be useful to 1) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data. | clinical neuroinformatics, dicom, magnetic resonance, image collection, clinical assessment, diagnose, healthy control, neuropsychological test, psychiatric disorder, schizoaffective disorder, schizophrenia, diffusion-weighted |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Mind Research Network - COINS |
Schizophrenia, Normal control | PMID:23760817 | COINS Data Use Agreement | nlx_155657 | SCR_002310 | 2026-08-04 09:40:37 | 33 | ||||||
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Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat Resource Report Resource Website 1+ mentions |
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat (RRID:SCR_002816) | Temporal-lobe.com | data set, data or information resource | Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection. | function, anatomical, connection, cortical, diagram, hippocampus, layer, neuroanatomy, neuroscience, parahippocampal, projection, subfield, temporal, lobe, topological, connectome, magnetic resonance, connectivity, formation, parahippocampal region, retrosplenial cortex, tract tracing |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Rat Hippocampus Atlas is related to: Integrated Manually Extracted Annotation has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway ; various independent donations |
PMID:21847380 PMID:19300446 |
Freely available, Account required | nif-0000-24805 | http://www.nitrc.org/projects/connectivity | SCR_002816 | Parahippocampal-hippocampal network, TEMPORAL-LOBE, Parahippocampal hippocampal connectivity | 2026-08-04 09:40:44 | 7 |
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