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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 |
nlx_156014 | SCR_000082 | 2025-02-14 10:29:11 | 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 | GNU Lesser General Public License | nlx_155663 | SCR_001751 | 2025-02-14 10:29:48 | 0 | |||||||
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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 | GNU Lesser General Public License | nlx_155575 | SCR_002252 | Magnetic Resonance Connectome Automated Pipeline, MR Connectome Automated Pipeline (MRCAP) | 2025-02-14 10:29:55 | 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 |
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 | 2025-02-14 10:29:36 | 54 | ||||||
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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 | 2025-02-14 10:29:35 | 102 | ||||||||
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PST MRI Simulator Resource Report Resource Website |
PST 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) | Commercial | 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 | 2025-02-14 10:29:59 | 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 |
GNU General Public License | nlx_155832 | http://www.nitrc.org/projects/nfg | SCR_002457 | Numerical Fibre Generator (NFG) | 2025-02-14 10:29:59 | 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) | Commercial | 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 | 2025-02-14 10:29:54 | 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 | 2025-02-14 10:30:33 | 35 | ||||||
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UNC-Wisconsin Neurodevelopment Rhesus MRI Database Resource Report Resource Website |
UNC-Wisconsin Neurodevelopment Rhesus MRI Database (RRID:SCR_014177) | A macaque brain MRI database characterizing the normal postnatal macaque brain development. This longitudinal primate database was acquired from a cohort of healthy macaque monkeys ranging from a few week olds up to 3-year-old adolescents. Each scan consists of structural (both T1 and T2) and diffusion MRI. | macaque, brain development, postnatal, diffusion mri, structural mir |
uses: UNC Primate Brain Atlas uses: AutoSeg is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Available to the research community | SCR_014177 | 2025-02-14 10:32:49 | 0 | |||||||||||
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SPIKECOR: fMRI tool for automated correction of head motion spikes Resource Report Resource Website 1+ mentions |
SPIKECOR: fMRI tool for automated correction of head motion spikes (RRID:SCR_014169) | This algorithm corrects for spikes in fMRI data, typically caused by abrupt head motion during scanning. It identifies outliers using Principal Component Analysis (PCA) in a sliding time-window; it is sensitive to global motion artifact, and stable against non-stationary signal changes. | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | SCR_014169 | 2025-02-14 10:32:37 | 2 | |||||||||||||
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ASL spm8 Resource Report Resource Website 1+ mentions |
ASL spm8 (RRID:SCR_008873) | ASL_spm8 | software resource | Quick ASL Wrapper for preprocessing arterial spin labeled (ASL) Data and computing blood flow measurements using UPenn ASL toolbox. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ASL data processing tool box |
GNU General Public License | nlx_155580 | SCR_008873 | 2025-02-14 10:31:31 | 1 | ||||||||
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ANTsR Resource Report Resource Website 10+ mentions |
ANTsR (RRID:SCR_008891) | ANTsR | software resource | An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data. | neuroimaging, multivariate statistical parametric mapping, dti, t1, image processing, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ANTS - Advanced Normalization ToolS |
BSD License | nlx_151365 | SCR_008891 | 2025-02-14 10:31:31 | 38 | ||||||||
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BRAINSConstellationDetector Resource Report Resource Website |
BRAINSConstellationDetector (RRID:SCR_012856) | BRAINSConstellationDetector | software resource | This program will find the mid-sagittal plane, the AC, PC, and mpj points in an image, and create an AC/PC aligned data set with the AC point at the center of the voxel lattice (la beled at the origin of the image physical space.) This work is an extention of the algorithms originally described by Dr. Babak A. Ardekani, Alvin H. Bachman, Model-based automatic detection of the anterior and posterior commissures on MRI scans, N euroImage, Volume 46, Issue 3, 1 July 2009, Pages 677-682, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2009.02.030. (http://www.sciencedirect.com/science/article/B6WNP-4VRP25C-4/2/8207b962a38aa83c822c6379bc43fe4c) | analyze, application, c++, dicom, fiducial, magnetic resonance, nifti, nrrd, registration, software, spatial transformation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
Creative Commons License | nlx_155697 | http://www.nitrc.org/projects/brainscdetector | SCR_012856 | 2025-02-14 10:32:25 | 0 | |||||||
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VIEWPixx Resource Report Resource Website 10+ mentions |
VIEWPixx (RRID:SCR_013271) | VIEWPixx | software resource | A complete display toolbox which has been conceived specifically to replace CRTs in vision science labs. The VIEWPixx features high-performance industrial LCD glass, and a panel controller which has been custom designed to support vision research.Our innovative LED backlight design features superior display uniformity, and a wide color gamut exceeding that of any CRT. In addition, it includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision. | eeg, meg, electrocorticography, experiment control, hardware, magnetic resonance, physiological recording, physiological stimulation, response monitoring, stimulus presentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155838 | http://www.nitrc.org/projects/crt_replacement | SCR_013271 | 2025-02-14 10:32:32 | 17 | |||||||
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Cerebral Blood Flow Database and Analysis Pipeline Resource Report Resource Website 1+ mentions |
Cerebral Blood Flow Database and Analysis Pipeline (RRID:SCR_009454) | CBFDAP | software resource | A web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CBFBIRN has parent organization: University of California at San Diego; California; USA |
BIRN License | nlx_155599 | SCR_009454 | 2025-02-14 10:31:33 | 2 | ||||||||
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DentalTools Resource Report Resource Website |
DentalTools (RRID:SCR_009463) | DentalTools | software resource | Software package that provides 3D imaging resources such as multimodal imaging, volume and mesh processing or segmentation for Dental Research. DentalTools package intends to contribute to the free exchange of information and methods in the dentistry research community. | domain independent | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | 3D Slicer License | nlx_155610 | SCR_009463 | 2025-02-14 10:31:34 | 0 | ||||||||
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caGWAS Resource Report Resource Website |
caGWAS (RRID:SCR_009617) | caGWAS | software resource | Too that allows researchers to integrate, query, report, and analyze significant associations between genetic variations and disease, drug response or other clinical outcomes. SNP array technologies make it possible to genotype hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously, enabling whole genome association studies. Within the Clinical Genomic Object Model (CGOM), the caIntegrator team created a domain model for Whole Genome Association Study Analysis. CGOM-caGWAS is a A semantically annotated domain model that captures associations between Study, Study Participant, Disease, SNP Association Analysis, SNP Population Frequency and SNP annotations. caGWAS APIs and web portal provide: * a semantically annotated domain model, database schema with sample data, seasoned middleware, APIs, and web portal for GWAS data; * platform and disease agnostic CGOM-caGWAS model and associated APIs; * the opportunity for developers to customize the look and feel of their GWAS portal; * a foundation of open source technologies; * a well-tested and performance-enhanced platform, as the same software is being used to house the CGEMS data portal; * accelerated analysis of results from various biomedical studies; and * a single application through which researchers and bioinformaticians can access and analyze clinical and experimental data from a variety of data types, as caGWAS objects are part of the CGOM, which includes microarray, genomic, immunohistochemistry, imaging, and clinical data. | application, computational neuroscience, genetic association, genomic analysis, imaging genomics, java, snp, gene, software, web environment, microarray, genomic, immunohistochemistry, imaging, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Cancer Institute |
BSD License | nlx_155841 | http://www.nitrc.org/projects/cagwas | SCR_009617 | caGWAS (Cancer Genome-Wide Association Studies), Cancer Genome-Wide Association Studies, CGOM-caGWAS | 2025-02-14 10:31:36 | 0 | ||||||
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NeuroWeb - NeuroImaging Database Resource Report Resource Website 1+ mentions |
NeuroWeb - NeuroImaging Database (RRID:SCR_009610) | NeuroWeb | software resource | Infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware. | computed tomography, magnetic resonance, pet, spect, mri, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155829 | http://www.nitrc.org/projects/neuroweb | SCR_009610 | 2025-02-14 10:31:29 | 1 | ||||||||
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MagPro Magnetic Stimulator Resource Report Resource Website 10+ mentions |
MagPro Magnetic Stimulator (RRID:SCR_009601) | MagPro | instrument resource | A complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry. | experiment control, hardware, magnetic resonance, response monitoring, stimulus presentation, clinical, neurophysiology, neurology, cognitive neuroscience, rehabilitation, psychiatry, instrument, equipment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is provided by: MagVenture |
Commercial license | nlx_155803 | http://www.nitrc.org/projects/magpro | SCR_009601 | MagPro Magnetic Stimulator (TMS) | 2025-02-14 10:31:36 | 10 |
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