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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MGH-USC Human Connectome Project Resource Report Resource Website 100+ mentions |
MGH-USC Human Connectome Project (RRID:SCR_003490) | MGH/UCLA HCP | data or information resource, instrument manufacture, material service resource, portal, production service resource, service resource | A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials. | human, structural, functional, neural, white matter, fiber, brain, in vivo, genomic, neuroimaging, visualization, neuroanatomy, genotype, connectivity, connectivity model, neural pathway, phenomic, connectomics, quantification, scanner, eeg, meg, shape analysis, spatial transformation, diffusion spectrum, q-ball, tensor metric, fiber tracking, connectome, behavior, scanner, web resource, diffusion spectrum, q-ball, tensor metric, quantification, shape analysis, spatial transformation, fiber tracking, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging has parent organization: Harvard Medical School; Massachusetts; USA has parent organization: NIH Human Connectome Project is parent organization of: USC Multimodal Connectivity Database |
Normal | NIH ; NIH Blueprint for Neuroscience Research |
Open unspecified license, (BSD/MIT-Style), LONI Software License, Public Domain | nif-0000-35789 | http://www.nitrc.org/projects/hcp_mgh-ucla | SCR_003490 | Harvard/MGH-UCLA Human Connectome Project, Harvard/MGH-UCLA Consortium: Human Connectome Project, HCP Harvard/MGH-UCLA, MGH/UCLA Consortium: Human Connectome Project | 2026-09-19 12:50:21 | 186 | ||||
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NeuroMorpho.Org Resource Report Resource Website 100+ mentions |
NeuroMorpho.Org (RRID:SCR_002145) | data or information resource, data repository, database, service resource, storage service resource | Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact. | neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurology, FASEB list |
is used by: NIF Data Federation is used by: BICCN is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: DONE: Detection of Outlier NEurons is related to: NIF Literature is related to: Computational Neurobiology and Imaging Center is related to: Integrated Manually Extracted Annotation is related to: xyz2swc is related to: Allen Institute for Brain Science has parent organization: George Mason University; Virginia; USA is parent organization of: NeuroMorpho.Org species ontology is parent organization of: NeuroMorpho.Org species ontology old |
MURI ONR N000141010198; NINDS R01 NS39600 |
PMID:17728438 PMID:16552417 PMID:18949582 |
Free, Available for download, Freely available | nif-0000-00006, r3d100010107 | http://www.nitrc.org/projects/neuromorpho_org, http://neuromorpho.org/, https://doi.org/10.17616/R3WW2K | SCR_002145 | Neuro Morpho, NeuroMorpho.org, NeuroMorpho | 2026-09-19 12:49:53 | 123 | |||||
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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) | 2026-09-19 12:49:55 | 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 |
NSF ; Swedish Foundation for Strategic Research ; Swedish Research Council |
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 | 2026-09-19 12:49:56 | 63 | ||||||
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Cognitive Paradigm Ontology Resource Report Resource Website 1+ mentions |
Cognitive Paradigm Ontology (RRID:SCR_002235) | CogPO | controlled vocabulary, data or information resource, ontology | Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. | functional neuroimaging, owl, cognition, behavior |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: BioPortal is related to: Human Imaging Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA has parent organization: Mind Research Network |
NIMH 1R01MH084812-01A1 | Free, Freely available | nlx_155537 | http://www.nitrc.org/projects/cogpo | SCR_002235 | 2026-09-19 12:49:55 | 9 | ||||||
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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 | 2026-09-19 12:49:55 | 140 | ||||||||
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NeuroImaging Analysis Kit (NIAK) Resource Report Resource Website |
NeuroImaging Analysis Kit (NIAK) (RRID:SCR_002497) | NIAK | data processing software, image processing software, software application, software library, software resource, software toolkit | Software library of modules and pipelines for fMRI processing with Octave or Matlab(r) that can run in parallel either locally or in a supercomputing environment. Linux OS and MINC file format are supported. NIAK currently includes a preprocessing, a region growing and a connectome pipelines. NIAK features powerful pipeline management capabilities, including parallel computing, generation of detailed logs and automatic handling of pipeline failures or updates. | reusable library, artifact removal, console (text based), constrained region growing, filtering, frequency domain, image-to-image, image-to-template, independent component analysis, intensity non-uniformity correction, intensity operations, intermodal, intrasubject, linear, matlab, minc, minc2, magnetic resonance, perl, posix/unix-like, principal component analysis, quality metrics, region growing, registration, regression, resampling, segmentation, spatial transformation, statistical operation, workflow, fmri, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155894 | http://www.nitrc.org/projects/niak | SCR_002497 | Neuroimaging Analysis Kit for Matlab and Octave | 2026-09-19 12:49:59 | 0 | ||||||
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Multiple Correlation Function Tool Resource Report Resource Website |
Multiple Correlation Function Tool (RRID:SCR_002321) | Multiple Correlation Function Tool | simulation software, software application, software resource | Software tool that provides a convenient environment to simulate NMR diffusion in closed pores. It builds on the eigenfunction expansion of the magnetization. | matlab, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD/MIT-Style Open unspecified license License | nlx_155670 | SCR_002321 | 2026-09-19 12:49:56 | 0 | ||||||||
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MisterI Resource Report Resource Website 1+ mentions |
MisterI (RRID:SCR_002317) | Mr. I, Mr I | data processing software, data visualization software, image processing software, software application, software resource | A powerful and modular medical image viewer/editor. It should be particularly useful to Undergraduates, Postdocs and Researchers in Medical Imaging to visualize data and to easily make attractive figures (for papers or presentations). It will also in a near future offer a number of advanced algorithms for medical image processing. Look at the video to get an idea ! http://www.benoitscherrer.com/MisterI/videos.html | c++, mgh/mgz, magnetic resonance, nifti, nrrd, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Cardware, Http://www.nitrc.org/include/glossary.php#697 | nlx_155666 | SCR_002317 | 2026-09-19 12:49:56 | 1 | ||||||||
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Microstructural correlation toolbox Resource Report Resource Website |
Microstructural correlation toolbox (RRID:SCR_002316) | MSC | software library, software resource, software toolkit | A Matlab-based software library to perform independent component analysis on group white matter skeleton generated by FSL TBSS. The script produces stable estimates of the white matter tract or tract segments that resemble highly correlated variation profiles across a group of subjects. | magnetic resonance, matlab, independent component analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at San Francisco; California; USA |
UCSF NCL Software License | nlx_155665 | SCR_002316 | 2026-09-19 12:49:56 | 0 | ||||||||
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MIAS Registration Toolkit Resource Report Resource Website |
MIAS Registration Toolkit (RRID:SCR_002312) | MIAS Toolkit | data processing software, image analysis software, registration software, software application, software resource | Software toolkit that provides the following libraries and functions on linux platform: # Multi-resolution registration of MR images include T1, multimodality, and DTI images. # The registration model is B-spline, and users can custermize their own image similarity measures by writing a plugin function and recompile the program. | magnetic resonance, dti, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | MIAS license, Http://www.nitrc.org/include/glossary.php#696 | nlx_155659 | SCR_002312 | 2026-09-19 12:49:56 | 0 | ||||||||
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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 | 2026-09-19 12:49:59 | 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) | 2026-09-19 12:50:01 | 59 | ||||||
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NFT Resource Report Resource Website 1+ mentions |
NFT (RRID:SCR_002450) | NFT | data processing software, image analysis software, segmentation software, software application, software resource, software toolkit | A MATLAB Toolbox for generating realistic head models from available data (MRI and/or electrode locations), for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic resonance (MR) images. The Boundary Element Method (BEM) and Finite Element Method (FEM) are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line. | eeg, meg, electrocorticography, eeg modeling, forward - inverse, modeling, matlab, mri, electrode |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Swartz Center for Computational Neuroscience |
PMID:20457183 | Free, Available for download, Freely available | nlx_155823 | http://www.nitrc.org/projects/nft | SCR_002450 | NFT: Neuroelectromag Forward Modeling, Neuroelectromagnetic Forward Modeling Toolbox, Neuroelectromagnetic Forward Head Modeling Toolbox | 2026-09-19 12:49:58 | 1 | |||||
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NCANDA: Data Integration Component Resource Report Resource Website 1+ mentions |
NCANDA: Data Integration Component (RRID:SCR_002447) | NCANDA-Datacore | data management, data or information resource, experimental protocol, narrative resource, software resource, training material | Manuals, training materials, and computational tools developed by the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA) Data Component. The NCANDA consortium consists of an Administrative Component at UC San Diego, the Data Integration Component at SRI International, and five data collection sites, Duke University, Oregon Health & Sciences University, SRI International, University of Pittsburgh, and UC San Diego. Each collection site will collect data from about 150 adolescents, each of them seen for one baseline and three annual follow-up visits. | clinical neuroinformatics, computational neuroscience, magnetic resonance, nifti, os independent, data integration, mri, bioinformatics, adolescent, alcohol, neurodevelopment |
uses: Lightweight Data Pipeline is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford Research Institute International |
PMID:26562597 PMID:24296908 |
Free, Available for download, Freely available | nlx_155821 | http://ncanda.sri.com | SCR_002447 | National Consortium on Alcohol and NeuroDevelopment in Adolescence: Data Integration Component | 2026-09-19 12:49:58 | 1 | |||||
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NIPY Resource Report Resource Website 10+ mentions |
NIPY (RRID:SCR_002489) | NIPY | data processing software, image analysis software, software application, software library, software resource, software toolkit | A complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI). | magnetic resonance, python, neuroimaging, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155883 | http://www.nitrc.org/projects/nipy | SCR_002489 | NIPY Structural and Functional Analysis | 2026-09-19 12:49:59 | 33 | ||||||
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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 | 2026-09-19 12:49:59 | 0 | |||||
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4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration Resource Report Resource Website |
4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration (RRID:SCR_002480) | 4D-PARSeR | data processing software, image analysis software, registration software, segmentation software, software application, software resource | A tool for analyzing 4D images with pathology. Originally developed for processing longitudinal images of patients with traumatic brain injury, the tool contains new image analysis algorithms that combine registration and segmentation in a coherent framework, accounting for extreme changes due to extensive tissue damage. | magnetic resonance, registration, segmentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Traumatic brain injury | Free, Freely avaialble | nlx_155870 | SCR_002480 | 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration), 4D-Pathological Anatomy Regression via Segmentation and Registration | 2026-09-19 12:49:59 | 0 | ||||||
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Group ICA Of EEG Toolbox Resource Report Resource Website 1+ mentions |
Group ICA Of EEG Toolbox (RRID:SCR_002478) | EEGIFT | data analysis software, data processing software, software application, software resource, software toolkit | Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher. | matlab, eeg, independent component analysis, magnetic resonance, algorithm |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Group ICA of fMRI Toolbox has parent organization: MIALAB - Medical Image Analysis Lab |
NIH ; NIBIB 1R01EB000840 |
PMID:21747835 | Available for download | nlx_155861 | http://www.nitrc.org/projects/gift | SCR_002478 | Group ICA Of EEG Toolbox (EEGIFT) | 2026-09-19 12:49:59 | 5 | ||||
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BrainVision Analyzer Resource Report Resource Website 100+ mentions |
BrainVision Analyzer (RRID:SCR_002356) | BVA | data analysis software, data processing software, software application, software resource | Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more. | Brain Products GmbH, neurophysiology, manage, data, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Products |
Commercially available | nlx_155717 | http://www.nitrc.org/projects/bva | SCR_002356 | BrainVision Analyzer, BrainVision Analyzer 2 | 2026-09-19 12:49:57 | 461 |
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