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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Harvard University; Cambridge; United States Resource Report Resource Website 500+ mentions |
Harvard University; Cambridge; United States (RRID:SCR_011273) | Harvard | university | Institution of higher education in the United States. Private Ivy League research university in Cambridge, Massachusetts. | research, private, undergraduate, graduate, master's, doctoral, phD, institution, university |
uses: ShareLaTeX uses: Overleaf uses: ReadCube uses: DIRECT2experts uses: Benchling uses: Writefull uses: Paperpile uses: GenomeCompiler is affiliated with: Broad Institute is related to: Beta Cell Biology Consortium is related to: ShareLaTeX is related to: CalR is related to: dcmqi is related to: PROMIS 2 MY Health is parent organization of: EGO - Eukaryotic Gene Orthologs is parent organization of: Drosophila RNAi Screening Center is parent organization of: FAS Center For Systems Biology is parent organization of: DF/HCC Health Communication Core is parent organization of: DF/HCC Specialized Histopathology Services Core is parent organization of: Harvard HSCI iPS Cell Core Facility is parent organization of: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility is parent organization of: Wyss Institute Imaging Core is parent organization of: Harvard FAS Bauer Core Laboratory is parent organization of: Harvard - Oxford Cortical Structural Atlas is parent organization of: Harvard Medical School, Department of Systems Biology: The Megason Lab - MegaCapture Software is parent organization of: Dataverse Network Project is parent organization of: edX is parent organization of: Authorea is parent organization of: BioNumbers is parent organization of: SNPHunter is parent organization of: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: Digital Access to Scholarship at Harvard is parent organization of: Data Scientist Training for Librarians is parent organization of: Arnold Arboretum of Harvard University: Weld Hill Microscopy Lab is parent organization of: Arnold Arboretum of Harvard University: Weld Hill Molecular Lab is parent organization of: 3D Slicer is parent organization of: GeneMerge is parent organization of: High Resolution Mouse Brain Atlas is parent organization of: Journal of Comparative Neurology Antibody database is parent organization of: FlyBase is parent organization of: CardioGenomics is parent organization of: Harvard Medical School Division of Medical Sciences is parent organization of: DPInteract is parent organization of: Gene Ontology Partition Database is parent organization of: MHCPEP is parent organization of: SDR: Specificity-Determining Residues in Protein Families is parent organization of: Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software is parent organization of: MedGene is parent organization of: New England Primate Research School is parent organization of: Boston Area Diabetes Endocrinology Research Center Metabolic Physiology and Energy Balance Core Facility is parent organization of: Harvard FAS Magnetic Resonance Laboratory is parent organization of: Cheng Li Lab of Computational Genomics is parent organization of: Motif Extractor is parent organization of: HIV Brain Sequence Database is parent organization of: Arnold Arboretum of Harvard University: Weld Hill Growth Facilities is parent organization of: HSDM Micro CT Core is parent organization of: DF/HCC Biostatistics Core Facility is parent organization of: DF/HCC Cancer Pharmacology Core is parent organization of: Dana Farber and Harvard Cancer Center Cancer Proteomics Center is parent organization of: DF/HCC Cell Manipulation Core Facility is parent organization of: DF/HCC Community Practice Research Core is parent organization of: DF/HCC High-Throughput Polymorphism Detection Core is parent organization of: DF/HCC Monoclonal Antibody Core is parent organization of: DF/HCC Pathology Specimen Locator is parent organization of: DF/HCC Rodent Histopathology Core Facility is parent organization of: DF/HCC Tissue Microarray and Imaging Core Facility is parent organization of: DF/HCC Tumor Imaging Metrics Core Facility is parent organization of: HMS Microfluidics Core Facility is parent organization of: HSCI Humanized Neonatal Mouse Center is parent organization of: Harvard Bioinformatics Core at Joslin Diabetes Center is parent organization of: Harvard CNS Imaging and Analysis Facility is parent organization of: Harvard CNS NNIN/C Computational Facility is parent organization of: Harvard CNS Nanofabrication Facility is parent organization of: Harvard CNS Nanomaterial Facility is parent organization of: Harvard Center for Biological Imaging is parent organization of: Harvard Digestive Diseases Center Biomedical CORE B: Microscopy and Histopathology is parent organization of: Harvard FAS Bauer Core: Mass Spectrometry and Proteomics Core Laboratory is parent organization of: Harvard FAS Center for Brain Science - Electron Microscopy Core Facility is parent organization of: Harvard PCMM Flow and Imaging Cytometry Resource is parent organization of: Harvard FAS Center for Brain Science - Imaging Core Facility is parent organization of: Harvard FAS Center for Brain Science - Neuroengineering Core Facility is parent organization of: Harvard FAS Center for Brain Science - Neuroimaging Core Facility is parent organization of: Harvard FAS Center for Crystallographic Studies is parent organization of: Harvard FAS Research Computing Core is parent organization of: Harvard FAS Small Molecule Mass Spectrometry Facility is parent organization of: Harvard PCPGM Genotyping Facility is parent organization of: Harvard Genome Modification Facility Harvard University is parent organization of: Harvard PCMM Optical Microscopy Core is parent organization of: Harvard PCPGM Biorepository for Medical Discovery is parent organization of: Harvard PCPGM Biosample Services Facility is parent organization of: Harvard PCPGM DNA Sequencing Facility is parent organization of: Harvard PCPGM Microarray Facility is parent organization of: Harvard Partners Research Computing Core is parent organization of: MGH HSCI-CRM Flow Cytometry Core Facility is parent organization of: Ragon Institute Biostatistics Core is parent organization of: Ragon Institute Imaging Core Flow Cytometry is parent organization of: Ragon Institute Imaging Core Microscopy is parent organization of: SERI Flow Cytometry Core Facility is parent organization of: Wyss Institute Machine Shop / 3D Prototyping Core is parent organization of: Wyss Institute Materials Characterization Core is parent organization of: Computational Biology and Functional Genomics Laboratory at Harvard is parent organization of: Harvard Medical School; Massachusetts; USA is parent organization of: Harvard T.H. Chan School of Public Health is parent organization of: Harvard Tumor Imaging Metrics Core Facility is parent organization of: Harvard SERI Graphic Services Core is parent organization of: Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics is parent organization of: Harvard University Labs and Facilities is parent organization of: HNDC Drug Discovery in Neurodegeneration is parent organization of: Eagle I is parent organization of: PolyPhen: Polymorphism Phenotyping is parent organization of: PLINK/SEQ is parent organization of: FreeSurfer is parent organization of: Magnaporthe comparative Database is parent organization of: CTSAconnect is parent organization of: International Stroke Database is parent organization of: International Stroke Database/Software is parent organization of: ChemBank is parent organization of: EM-DECODER is parent organization of: Ruby NIfTI is parent organization of: CummeRbund is parent organization of: BINOCh is parent organization of: Harvard Digestive Disease Center is parent organization of: GraPhlAn is parent organization of: biobakery is parent organization of: DeepNeuro is parent organization of: Joslin Diabetes Center is parent organization of: PAGODA is parent organization of: Harvard School of Public Health Microbiome Analysis Core Facility is parent organization of: Diffusion Toolkit is parent organization of: Cistrome is parent organization of: ADMIXTOOLS is parent organization of: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation is parent organization of: Harvard Medical School PCMM Microscopy Core Facility is parent organization of: PolicyModels is parent organization of: Cistrome is parent organization of: Biofactoid is parent organization of: Camera Control project is parent organization of: Harvard University Bauer Core Facility is parent organization of: Harvard Tissue Atlas is parent organization of: Harvard Medical School Center for Cancer Systems Pharmacology is parent organization of: SPRING is parent organization of: Minerva is parent organization of: scimap is parent organization of: moseq2-app is parent organization of: Keypoint MoSeq is parent organization of: Harvard University Chan School of Public Health Bioinformatics Core Facility is parent organization of: VenomView |
SCR_016676, Wikidata:Q13371, ISNI:000000041936754X, Crossref funder ID:100007229, nlx_90063, grid.38142.3c | https://ror.org/03vek6s52 | SCR_011273 | Harvard University | 2026-08-01 12:04:24 | 728 | |||||||
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MR Connectome Automated Pipeline Resource Report Resource Website |
MR Connectome Automated Pipeline (RRID:SCR_002252) | MRCAP | software resource | Based on JIST and MIPAV, this pipeline combines structural magnetic resonance data with diffusion tensor imaging to estimate a connectome, which is a comprehensive description of the wiring diagram of the brain. | java, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit is related to: MIPAV: Medical Image Processing and Visualization |
PMID:22481745 | Free, Available for download, Freely available | nlx_155575 | SCR_002252 | Magnetic Resonance Connectome Automated Pipeline, MR Connectome Automated Pipeline (MRCAP) | 2026-08-01 12:01:44 | 0 | ||||||
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International Neuroinformatics Coordinating Facility Resource Report Resource Website 50+ mentions |
International Neuroinformatics Coordinating Facility (RRID:SCR_002282) | INCF | nonprofit organization | Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society. | neuroinformatics, neuroscience, neuroimaging, clinical, brain, data, sharing, reuse, global |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Spike Sorting Evaluation Project is related to: Allen Brain Atlas API is related to: SenseLab has parent organization: Karolinska Institute; Stockholm; Sweden has parent organization: Royal Institute of Technology; Stockholm; Sweden is parent organization of: INCF Dataspace is parent organization of: Waxholm Space is parent organization of: MUlti SImulation Coordinator is parent organization of: INCF Software Center is parent organization of: Program on Ontologies of Neural Structures is parent organization of: Common Upper Mammalian Brain Ontology is parent organization of: INCF Training in Neuroinformatics is parent organization of: INCF Funding is parent organization of: INCF Blog is parent organization of: INCForg - YouTube is parent organization of: INCF Swiss Node is parent organization of: INCF Newsroom is parent organization of: INCF Japan Node is parent organization of: Scalable Brain Atlas is parent organization of: INCF Job Board is parent organization of: INCF Neuroimaging Data Sharing is parent organization of: Waxholm Space is parent organization of: NeuroLex is parent organization of: Neuroimaging Data Model is parent organization of: Neuron Registry Curator Interface is parent organization of: INCF-Neurobot |
Swedish Research Council ; Swedish Foundation for Strategic Research ; NSF |
ISNI: 0000 0004 6107 939X, grid.498423.0, nif-0000-00365 | https://ror.org/02y5xjh56 | SCR_002282 | INCF, International Neuroinformatics Coordinating Facility, The International Neuroinformatics Coordinating Facility | 2026-08-01 12:02:09 | 56 | ||||||
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CleanLine Resource Report Resource Website 100+ mentions |
CleanLine (RRID:SCR_002233) | CleanLine | software resource | An EEGLAB plugin which adaptively estimates and removes sinusoidal artifacts from independent component analysis (ICA) components or scalp channels using a frequency-domain (multi-taper) regression technique with a Thompson F-statistic for identifying significant sinusoidal artifacts. This approach has been advocated by Partha Mitra and Hemant Bokil (Observed Brain Dynamics, Chapter 7.3.4., 2007) and CleanLine utilizes modified routines from the Mitra Lab's Chronux Toolbox (www.chronux.org). Sinusoidal noise can be a prominent artifact in recorded electrophysiological data. This can stem from AC power line fluctuations (e.g. 50/60 Hz line noise + harmonics), power suppliers (e.g. in medical equipment), fluorescent lights, etc. Notch filtering is generally undesirable due to creation of band-holes, and significant distortion of frequencies around the notch frequency (as well as phase distortion at other frequencies and Gibbs rippling in the time-domain). | eeg, meg, electrocorticography, spectral analysis, temporal transformation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155529 | SCR_002233 | 2026-08-01 12:02:08 | 120 | ||||||||
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PSTNet: MRI Simulator Resource Report Resource Website |
PSTNet: MRI Simulator (RRID:SCR_002460) | MRI Simulator | instrument resource | MRI Simulator that provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children, the elderly, and psychiatric patients, are often prone to claustrophobia and anxiety in the bore of a magnet, and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5%, improving cost effectiveness. | experiment control, hardware, magnetic resonance, training, simulator, mri, scanner, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Restricted | https://drive.google.com/file/d/1ZMEBlvJqOupTbVemgrdVN66Bf6Xa2Dhr/view?usp=drivesdk | nlx_155834 | http://www.nitrc.org/projects/mri_simulator, https://pstnet.com/wp-content/uploads/2018/05/MRI-Simulator-Pamphlet-.pdf | SCR_002460 | Psychology Software Tools MRI Simulator | 2026-08-01 12:01:48 | 0 | |||||
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Numerical Fibre Generator Resource Report Resource Website 50+ mentions |
Numerical Fibre Generator (RRID:SCR_002457) | NFG | software resource | A collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them. Its primary use is to enable the testing of tracking algorithms | analyze, c, console (text based), macos, microsoft, magnetic resonance, posix/unix-like, tractography, windows, dw-mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Research Institute |
Free, Available for download, Freely available | nlx_155832 | http://www.nitrc.org/projects/nfg | SCR_002457 | Numerical Fibre Generator (NFG) | 2026-08-01 12:01:48 | 58 | ||||||
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MRI Digital Projection System Resource Report Resource Website |
MRI Digital Projection System (RRID:SCR_002486) | Hyperion | instrument resource | MRI Digital Projection System that uses Digital Light Processing (DLP) technology providing microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images. Includes: * High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor * Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room * 30 meter fiber optic cable that runs between the projector and projector control station * Heavy duty, magnet compatible, projector stand (assembly required) * Heavy duty, magnet compatible mirror stand with mirror (assembly required) * High resolution, lenticular pitch rear projection screen for high quality image reproduction * Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended) | experiment control, hardware, magnetic resonance, stimulus presentation, mri, projector, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Restricted | https://drive.google.com/file/d/1OPZZ054sMCqq-z1Fiuof2gEoLkK8Knp6/view?usp=drivesdk | nlx_155879 | http://www.nitrc.org/projects/projector, https://pstnet.com/wp-content/uploads/2018/08/2018ProductSheetHyperion.pdf | SCR_002486 | Hyperion MRI Digital Projection System | 2026-08-01 12:02:08 | 0 | |||||
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Medical Image Processing and Visualization in Virtual Environments Resource Report Resource Website |
Medical Image Processing and Visualization in Virtual Environments (RRID:SCR_001751) | Medical Image Processing and Visualization in Virtual Environments | software resource | This resouce will centralize development of tools for interaction with medical imaging data in immersive virtual environments (based on the Vizard platform). | magnetic resonance, python, medical, imaging, virtual environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:11020811 | Free, Freely available | nlx_155663 | SCR_001751 | 2026-08-01 12:01:49 | 0 | |||||||
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PyNIfTI Resource Report Resource Website 1+ mentions |
PyNIfTI (RRID:SCR_000693) | software resource | PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays. | reusable library, analyze, magnetic resonance, nifti, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NiBabel has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
Free, Available for download, Freely available | nlx_155929 | http://www.nitrc.org/projects/pynifti | SCR_000693 | PyNIfTI - Pythonic access to NIfTI and ANALYZE files, Pythonic access to NIfTI and ANALYZE files | 2026-08-01 12:01:28 | 2 | |||||||
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GesTr Resource Report Resource Website |
GesTr (RRID:SCR_000857) | GesTr | software resource | A cross platform, open source gesture tracking program. You launch it from the web, and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons. GesTr supports simple XML files to customize recognized gestures and their corresponding actions. GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device. | domain independent, gesture, tracking | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155637 | SCR_000857 | 2026-08-01 12:01:19 | 0 | ||||||||
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Data Format Tools Resource Report Resource Website |
Data Format Tools (RRID:SCR_000856) | DFT | software resource | A loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand. | console (text based), dicom, format conversion, macos, magnetic resonance, nifti, posix/unix-like, python, system administrators, visualization, web environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155608 | SCR_000856 | 2026-08-01 12:01:26 | 0 | ||||||||
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VectorValuedHistogramNormalizer Resource Report Resource Website |
VectorValuedHistogramNormalizer (RRID:SCR_000082) | VectorValuedHistogramNormalizer | software resource | Software tool for MRI intensity standardization by aligning histograms of higher dimensions. The methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf are implemented as and ITK filter. | magnetic resonance, mri, standardization, histogram, intensity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: INCF Software Center has parent organization: University of Erlangen-Nuremberg; Bavaria; Germany |
Free, Freely Avaliable | nlx_156014 | SCR_000082 | 2026-08-01 12:01:08 | 0 | ||||||||
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MouseTracker Resource Report Resource Website 10+ mentions |
MouseTracker (RRID:SCR_005979) | MouseTracker | software resource | A free, user-friendly software package that allows researchers to record and analyze hand movements traveling toward potential responses on the screen (via the x, y coordinates of the computer mouse). By looking at the dynamics of how participants' hand movements settle into a response alternative--and how they may be partially pulled toward other alternatives--researchers glean valuable information about real-time cognitive processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. MouseTracker has impressive temporal resolution, comparable to eye-tracking and event-related brain potential (ERP) measures. Experiments can incorporate images, letter strings, sounds, and videos. Once recorded, mouse trajectories can be visualized, averaged, and explored, and measures of attraction/curvature, complexity, velocity, and acceleration can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, cognitive science, and beyond. | magnetic resonance, movement |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Dartmouth College; New Hampshire; USA |
Free, Non-commercial | nlx_151359 | http://www.nitrc.org/projects/mousetracker | SCR_005979 | Mouse Tracker | 2026-08-01 12:03:04 | 37 | ||||||
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Neuroimaging Informatics Technology Initiative Resource Report Resource Website 100+ mentions |
Neuroimaging Informatics Technology Initiative (RRID:SCR_003141) | NIfTI | knowledge environment, training resource | Coordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics tools | neuroimaging, neuroinformatics, technology, service, training, research, mri, fmri, software, algorithm or reusable library, c, computed tomography, developers, information resource, java, matlab, magnetic resonance, nifti, other information resource, pet, spect, software |
is used by: Stark Cross-Sectional Aging is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: GIFTI has parent organization: National Institute of Mental Health is parent organization of: NIfTI Data Format Working Group |
NIH Blueprint for Neuroscience Research ; NIMH ; NINDS |
Free, Freely available | nif-0000-00561 | http://www.nitrc.org/projects/nifti | http://www.bic.mni.mcgill.ca/nifti/ | SCR_003141 | NIfTI: Neuroimaging Informatics Technology Initiative, Neuroimaging Informatics Technology Initiative (NIfTI) | 2026-08-01 12:10:43 | 309 | ||||
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Parkinson's Progression Markers Initiative Resource Report Resource Website 500+ mentions |
Parkinson's Progression Markers Initiative (RRID:SCR_006431) | PPMI | biomaterial supply resource, material resource | An observational longitudinal clinical study partnership to identify and validate biomarkers of Parkinson disease (PD) progression and provide easy and open web-based access to the comprehensive set of correlated clinical data and biospecimens, information, and biosamples acquired from PD and age and gender matched healthy control subjects to the research community. The data and specimens have been collected in a standardized manner under strict protocols and includes clinical (demographic, motor and non-motor, cognitive and neurobehavioral), imaging (raw and processed MRI, SPECT and DAT), and blood chemistry and hematology subject assessments and biospecimen inventories (serum, plasma, whole blood, CSF, DNA, RNA and urine). All data are de-identified to protect patient privacy. PPMI will be carried out over five years at 21 clinical sites in the United States and Europe and requires the participation of 400 Parkinson's patients and 200 control participants. The PPMI database provides researchers with access to correlated clinical and imaging data, along with annotated biospecimens, all available within an open access system that encourages data sharing (http://www.ppmi-info.org/access-data-specimens/). The website hosts an Ongoing Analysis section to keep the scientific community apprised of analyses being completed, in hopes of stimulating collaborations between researchers who are using PPMI data and specimens. | analyze, atlas data, clinical neuroinformatics, computational neuroscience, dicom, imaging genomics, loni pipeline, minc, magnetic resonance, pet, spect, dat, image collection, clinical, biological, imaging data, biomarker, imaging, demographic, motor, cognitive, neurobehavioral, hematology, consortium, biosample, sleep, longitudinal, FASEB list |
is used by: Biomarkers Across Neurodegenerative Diseases is listed by: Consortia-pedia is listed by: One Mind Biospecimen Bank Listing is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: NIH Data Sharing Repositories is related to: NIH Data Sharing Repositories has parent organization: Laboratory of Neuro Imaging has parent organization: Michael J. Fox Foundation for Parkinsons Research |
Parkinson's disease, Control | Michael J. Fox Foundation for Parkinsons Research ; consortium of industry partners ; non-profit organizations ; private individuals |
Open unspecified license, Application required | nlx_33115 | http://www.nitrc.org/projects/ppmi | SCR_006431 | Parkinson's Progression Markers Initiative | 2026-08-01 12:10:52 | 730 | ||||
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NITRC GForge Extensions Resource Report Resource Website 1+ mentions |
NITRC GForge Extensions (RRID:SCR_002495) | software resource, software repository | Software repository of custom extensions to the GForge collaborative environment. | custom extension, gforge collaborative environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIBIB N02-EB-6-4281 | PMID:18999128 | Free, Available for download, Freely available | nlx_155891 | SCR_002495 | 2026-08-02 09:03:32 | 1 | |||||||
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VMTK in 3D Slicer Resource Report Resource Website 1+ mentions |
VMTK in 3D Slicer (RRID:SCR_002579) | software toolkit, software resource | Provides series of modules which enable functions of Vascular Modeling Toolkit in 3D Slicer. Functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.VMTK is available through the extension manager for 3D Slicer from version 4.6.2. Main difference to Slicer3 version is that now all VMTK modules come as one extension bundle. This should enhance the installation experience for users. | Vascular Modeling Toolkit, 3D Slicer, vessel enhancement filtering, level set segmentation, centerline computation, network extraction, branch splitting, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: Insight Segmentation and Registration Toolkit is related to: Vascular Modeling Toolkit |
Free | SCR_014179, nlx_155981 | https://github.com/haehn/VMTKSlicerExtension, http://www.nitrc.org/projects/slicervmtklvlst | http://www.vmtk.org/Main/VmtkIn3DSlicer | SCR_002579 | Slicer4:VMTK, Vascular Modeling Toolkit in 3D Slicer 4, VMTK Extension for 3D Slicer 4.2+, VMTK in 3D Slicer 4, Vascular Modeling Toolkit in 3D Slicer | 2026-08-02 09:03:32 | 1 | ||||||
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Network Based Statistic Toolbox Resource Report Resource Website 50+ mentions |
Network Based Statistic Toolbox (RRID:SCR_002454) | NBS | software toolkit, software resource | Matlab toolbox for testing hypotheses about the human connectome. NBS has been widely used to identify connections and networks comprising the connectome that are associated with an experimental effect or a between-group difference. User provides a series of connectivity matrices from different cohorts, or from the same subject during different experimental conditions. Connectivity matrices are inferred from neuroimaging data using other packages that, for example, count the number of tractography streamlines that interconnect each pair of regions (diffusion-MRI), or measure the extent of inter-regional correlation in BOLD response (fMRI). User specifies hypothesis to be tested at every connection with the general linear model. Features include: graphical user interface; NBSview, a basic network viewer modeled on SPMresults; exchange blocks for repeated measures; options to measure network size with intensity or extent; false discovery rate (FDR) option. Developed by Zalesky, Fornito, Cocchi and Bullmore. | connectivity analysis, domain independent, statistical operation, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Network-Based R-Statistics has parent organization: University of Melbourne; Victoria; Australia |
PMID:20600983 | Free, Available for download, Freely available | nlx_155826 | http://www.nitrc.org/projects/nbs | SCR_002454 | Network Based Statistic Toolbox, Network-Based Statistic (NBS) | 2026-08-02 09:03:20 | 56 | |||||
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INCF Software Center Resource Report Resource Website 1+ mentions |
INCF Software Center (RRID:SCR_002347) | INCF Software Center | software resource, software repository | Software repository that makes it easy for neuroscientists to find, use and share software tools. The Software Center is accessible to everyone: you can browse and download available software tools without registering. However, by creating an account, you will be able to post comments, and request to join development teams. The INCF Software Center and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are sharing content. Software tools hosted by NITRC also appear at the INCF Software Center. Your software tool will be available to all users of the Software Center. You will be able to upload documentation, executables and related files; track use of your software; create a wiki; and establish a development team. Registered Software Center users will be able to comment on and post reviews about your software, and can request to join your development team. INCF's vision of the Software Center is that it will become a communication enabler for software users as well as developers. Accordingly, future system features to be added include communication and collaboration functions. We also plan to include support services to allow software developers organize their software, track the use, and receive feedback for further improvement and development. Further development of the Software Center will be strongly driven by the user needs. Please let us know what features you would like to see added. | neuroscience, software, database |
lists: 3DSlicerLupusLesionModule lists: BRAINSCut lists: BRAINSCortex lists: Sumatra is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VectorValuedHistogramNormalizer is related to: NITRC Community Conferences Workshops and Meetings is related to: Automatic Segmentation Tool Adapter is related to: R-package for adaptive DWI analysis is related to: R-package for adaptive fMRI analysis is related to: REX is related to: SPHARM-PDM Toolbox is related to: Brain lesion segmentation tool using SVM is related to: UNC Human Brain Atlas is related to: ValMap: simple statistical mapping tool is related to: DW-MRI Random Walk Simulator is related to: NeuronVisio is related to: Brainvox is related to: JIST Resources for Algorithm Development is related to: BRAINSDemonWarp is related to: BrainMask Volume Processing Tool is related to: DTI BrainImageScope is related to: ProbabilisticBiasCorrection is related to: BrainCSI is related to: Slicer3 Example Modules is related to: TOADS-CRUISE Brain Segmentation Tools is related to: ABC (Atlas Based Classification) is related to: Whole Brain Catalog is related to: BrainVisa Morphology extensions has parent organization: International Neuroinformatics Coordinating Facility is parent organization of: PANDORA Matlab Toolbox |
The community can contribute to this resource | nif-0000-00372 | SCR_002347 | International Neuroinformatics Coordinating Facility Software Center | 2026-08-02 09:03:30 | 8 | |||||||
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Create DWI Atlas Resource Report Resource Website |
Create DWI Atlas (RRID:SCR_009455) | Create DWI Atlas | software toolkit, software resource | This package is a set of three slicer modules which together are able to compute a DWI Atlas given a set of DWI''s. The modules included are: # A Groupwise Registration module -> compute''s a deformation field for each DWI, using, for example, FA maps as input # Warp DWI module -> used to warp each DWI using the deformation from (1) # DWI Averager -> used to average the set of warped DWI''s producing the final DWI Atlas | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | 3D Slicer License | nlx_155601 | SCR_009455 | 2026-08-02 09:05:35 | 0 |
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