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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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3D Slicer Resource Report Resource Website 1000+ mentions |
3D Slicer (RRID:SCR_005619) | Slicer | software application, data processing software, data visualization software, image analysis software, software resource | A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl. | birn, diffusion, functional, na-mic (ncbc), nifti-1 support, registration, segmentation, visualization, volume, warping |
uses: 3DSlicerLupusLesionModule uses: ShapePopulationViewer uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Slicer3 Example Modules is related to: Stereoscopic Atlas of Intrinsic Brain Networks is related to: VMTK in 3D Slicer is related to: Diffusion Tractography with Kalman Filter is related to: Fast Nonlocal Means for MRI denoising is related to: SpineSegmentation module for 3DSlicer is related to: BioImage Suite is related to: NA-MIC Kit is related to: Hammer And WML Modules for 3D Slicer is related to: ABC (Atlas Based Classification) is related to: ARCTIC is related to: Finsler tractography module for Slicer is related to: GAMBIT is related to: GPU based affine registration is related to: GTRACT is related to: LEAD-DBS has parent organization: Harvard University; Cambridge; United States is parent organization of: Level-set Segmentation for Slicer3 is parent organization of: Slicer3 Module Rician noise filter has plug in: MultiXplore works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: SlicerMorph |
NIH ; NCRR ; NIBIB ; NCI ; US Army ; Telemedicine and Advanced Technology Research Center |
3D Slicer License | nif-0000-00256 | http://www.nitrc.org/projects/slicer | SCR_005619 | Slicer, 3D Slicer: A multi-platform free and open source software package for visualization and medical image computing, 3D Slicer, 3DSlicer | 2026-02-16 09:46:30 | 2238 | |||||
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Human Imaging Database Resource Report Resource Website 1+ mentions |
Human Imaging Database (RRID:SCR_006126) | HID | software application, image repository, data management software, data repository, software resource, storage service resource, database, source code, service resource, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2017. Database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. The HID can be extended to contain relevant information concerning experimental subjects, assessments of subjects, the experimental data collected, the experimental protocols, and other metadata normally included with experiments. |
imaging, fmri, clinical, behavior, biomedical imaging data, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cognitive Paradigm Ontology is related to: XCEDE Schema has parent organization: Biomedical Informatics Research Network |
Schizophrenia | PMID:19826494 PMID:18348946 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00269 | http://www.nitrc.org/projects/hid | http://fbirnbdr.nbirn.net:8080/BDR/ | SCR_006126 | fBIRN Data Repository, Human Imaging Database (HID) System, Function BIRN Data Repository | 2026-02-16 09:46:37 | 3 | |||
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Automated Image Registration Resource Report Resource Website 10+ mentions |
Automated Image Registration (RRID:SCR_005944) | AIR | software application, data processing software, software toolkit, registration software, software library, image analysis software, software resource, alignment software | A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs. | registration, alignment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps |
GNU General Public License | nif-0000-00260 | http://www.nitrc.org/projects/air | SCR_005944 | 2026-02-16 09:46:35 | 29 | |||||||
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BrainImage Software Resource Report Resource Website 1+ mentions |
BrainImage Software (RRID:SCR_006139) | BrainImage | software application, data processing software, image processing software, image analysis software, software resource | A multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can: * Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes. * Create and display triangular mesh surfaces from MRI volumes. * Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display. * Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit. This 3D image processing and analysis program for the Apple Macintosh PowerPC is based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. The last version of the software included multiplatform capability, volume visualization and advanced image analysis tools. | mri, segmentation, visualization, volume, neuroimaging, analyze, anatomic, application, artifact removal, image display, java, labeling, macos, mesh generation, microsoft, modeling, magnetic resonance, quantification, region of interest, rendering, spatial transformation, three dimensional display, volume measurement, volumetric analysis, volumetric analysis, windows, platform |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: NIH Image has parent organization: Stanford University School of Medicine; California; USA |
Human Brain Project | GNU General Public License | nif-0000-00272 | http://spnl.stanford.edu/tools/brainimage.htm | SCR_006139 | Brain Image, BrainImageJ, BrainImageJava | 2026-02-16 09:46:38 | 8 | |||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | software application, data processing software, image processing software, image analysis software, software resource | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-02-16 09:46:39 | 1 | ||||||||
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Segmentation of Hippocampus Subfields Resource Report Resource Website 1+ mentions |
Segmentation of Hippocampus Subfields (RRID:SCR_005996) | ASHS | software application, data processing software, image analysis software, software resource, segmentation software | A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL | hippocampus, mri, t1-weighted image, t2-weighted image, ca1, ca2, ca3, statistical modeling, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ANTS - Advanced Normalization ToolS is related to: FSL has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:19405131 PMID:20600984 |
GNU General Public License | nlx_151370 | http://www.nitrc.org/projects/ashs | SCR_005996 | Automatic Segmentation of Hippocampal Subfields, HippocampalSubfieldSegmentation | 2026-02-16 09:46:36 | 7 | |||||
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Artifact Detection Tools Resource Report Resource Website 100+ mentions |
Artifact Detection Tools (RRID:SCR_005994) | ART | software application, data processing software, software toolkit, image processing software, image analysis software, software resource | Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well. * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE | artifact removal, quality metrics, registration, motion analysis, neuroimaging, fmri, spike, motion, artifact, timeseries, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: RapidArt has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Free, Available for download | nlx_151369 | http://www.nitrc.org/projects/artifact_detect | SCR_005994 | 2026-02-16 09:46:36 | 204 | |||||||
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Allen Brain Atlas API Resource Report Resource Website 10+ mentions |
Allen Brain Atlas API (RRID:SCR_005984) | Allen Brain Atlas API | software application, software resource, topical portal, source code, portal, data or information resource | API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service | atlas application, expression data, 3d volume, 3d coordinate, gene, reference atlas, connectivity, histology, microarray, brain, rna sequencing, mri, dti, api, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics, ish, high resolution image, nissl, annotation, atlas, image, web service, neuroblast, gene expression, gene, computational neuroscience, mouse brain, neuroanatomy, neuroimaging, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Mouse Brain Reference Atlas is related to: Allen Developing Mouse Brain Atlas is related to: International Neuroinformatics Coordinating Facility is related to: Brain Explorer Atlas and Teaching Tool is related to: CellTax vignette is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science |
Other/Commercial license License | nlx_151358 | http://www.nitrc.org/projects/incf_allen-brai | SCR_005984 | 2026-02-16 09:46:35 | 13 | |||||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | software application, data processing software, data management software, software resource, collaboration tool | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-02-16 09:46:35 | 14 | |||||
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Hammer And WML Modules for 3D Slicer Resource Report Resource Website 1+ mentions |
Hammer And WML Modules for 3D Slicer (RRID:SCR_005980) | HAMMER, hammerwml | software application, data processing software, registration software, image analysis software, software resource, segmentation software | A software plugin for 3D Slicer that matches morphological signatures of medical images automatically. HAMMER is an acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration (Dinggang Shen, Christos Davatzikos, HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, IEEE Trans. on Medical Imaging, 21(11):1421-1439, Nov 2002) - an elastic registration algorithm for medical images, matching morphological signatures of images in a hierarchical multi-scale regime. White matter lesion (WML) segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w, T2-w, PD-w and FLAIR MR brain images. (Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008). | mri, registration, white matter lesion, segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:12575879 PMID:18280928 |
3D Slicer License | nlx_151352 | http://www.nitrc.org/projects/hammerwml | SCR_005980 | HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, Hierarchical Attribute Matching Mechanism for Elastic Registration and White matter lesion Modules for 3D Slicer | 2026-02-16 09:46:35 | 1 | |||||
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ABC (Atlas Based Classification) Resource Report Resource Website 1+ mentions |
ABC (Atlas Based Classification) (RRID:SCR_005981) | ABC | software application, data processing software, image analysis software, software resource, workflow software | A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput. | brain, image, image registration, filter, segmentation, inhomogeneity correction, beta, c++, linux, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is related to: INCF Software Center has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of Utah; Utah; USA |
3D Slicer License | nlx_151362 | SCR_005981 | 2026-02-16 09:46:42 | 3 | ||||||||
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Computerized Anatomical Reconstruction and Editing Toolkit Resource Report Resource Website 50+ mentions |
Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) | CARET | software application, data processing software, data visualization software, image processing software, software resource | Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems. | reconstruction, visualization, cerebral cortex, surface, brain, dataset, cerebellar cortex, atlas application, mesh generation, quantitative shape analysis, segmentation, shape analysis, intersubject, image-to-template, gaussian curvature, mean curvature, animation, three dimensional display, two dimensional display, surface rendering, cortical flat map, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SumsDB has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIMH R01 MH60974; NEI EY02091 |
PMID:11522765 | Free, Available for download, Freely available | nif-0000-00279 | http://www.nitrc.org/projects/caret https://sources.debian.org/src/caret/ |
SCR_006260 | Computerized Anatomical Reconstruction Editing Toolkit | 2026-02-16 09:46:40 | 57 | ||||
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Stark Cross-Sectional Aging Resource Report Resource Website |
Stark Cross-Sectional Aging (RRID:SCR_014171) | data set, data or information resource | Behavioral and imaging data from about 120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes traditional neuropsycholgical measures, hippocampal-specific behavioral measures, whole-brain DTI, high-resolution DTI of the medial temporal lobes, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields. | data set, aging, hippocampus, behavioral, dti, mri, image |
uses: Neuroimaging Informatics Technology Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
NIA R01 AG034613 | Available to the research community | SCR_014171 | 2026-02-16 09:48:32 | 0 | |||||||||
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YMDTI: Diffusion Tensor Images of Healthy Young Males Resource Report Resource Website |
YMDTI: Diffusion Tensor Images of Healthy Young Males (RRID:SCR_014183) | YMDTI | data set, data or information resource | A dataset which contains diffusion tensor images of 93 healthy, young male subjects. | data set, diffusion tensor image, young male subject | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014183 | Diffusion Tensor Images of Healthy Young Males | 2026-02-16 09:48:29 | 0 | ||||||||
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Epilepsy T1 and Hippocampal Segmentation Datasets Resource Report Resource Website |
Epilepsy T1 and Hippocampal Segmentation Datasets (RRID:SCR_014926) | data set, data or information resource | Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site. | hippocampus, t1, dataset, skull stripped, mri, segmented hippocampus, epilepsy, temporal lobe epilepsy, tle | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_014926 | 2026-02-16 09:48:39 | 0 | ||||||||||
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COBRE Resource Report Resource Website 100+ mentions |
COBRE (RRID:SCR_010482) | COBRE | data set, data or information resource | Data set of raw anatomical and functional MR data from 72 patients with Schizophrenia and 75 healthy controls (ages ranging from 18 to 65 in each group). All subjects were screened and excluded if they had: history of neurological disorder, history of mental retardation, history of severe head trauma with more than 5 minutes loss of consciousness, history of substance abuse or dependence within the last 12 months. Diagnostic information was collected using the Structured Clinical Interview used for DSM Disorders (SCID). A multi-echo MPRAGE (MEMPR) sequence was used with the following parameters: TR/TE/TI = 2530/(1.64, 3.5, 5.36, 7.22, 9.08)/900 ms, flip angle = 7��, FOV = 256x256 mm, Slab thickness = 176 mm, Matrix = 256x256x176, Voxel size =1x1x1 mm, Number of echos = 5, Pixel bandwidth =650 Hz, Total scan time = 6 min. With 5 echoes, the TR, TI and time to encode partitions for the MEMPR are similar to that of a conventional MPRAGE, resulting in similar GM/WM/CSF contrast. Rest data was collected with single-shot full k-space echo-planar imaging (EPI) with ramp sampling correction using the intercomissural line (AC-PC) as a reference (TR: 2 s, TE: 29 ms, matrix size: 64x64, 32 slices, voxel size: 3x3x4 mm3). Slice Acquisition Order: Rest scan - collected in the Axial plane - series ascending - multi slice mode - interleaved MPRAGE - collected in the Sag plane - series interleaved - multi slice mode - single shot The following data are released for every participant: * Resting fMRI * Anatomical MRI * Phenotypic data for every participant including: gender, age, handedness and diagnostic information. | resting fmri, anatomical mri, phenotype, gender, age, handedness, diagnosis, adult human, fmri, mri, neuroimaging, mental state assessment, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Mind Research Network has parent organization: 1000 Functional Connectomes Project has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Schizophrenia, Normal control, Aging | NCRR 1P20RR021938-01A2 | Creative Commons Attribution-NonCommercial License, Account required | nlx_157762 | SCR_010482 | Center for Biomedical Research Excellence, Center for Biomedical Research Excellence (COBRE) | 2026-02-16 09:47:48 | 108 | |||||
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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 | 2026-02-14 02:00:21 | 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 | 2026-02-14 02:00:21 | 120 | ||||||||
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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) | Restricted | 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 | 2026-02-14 02:00:17 | 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) | 2026-02-14 02:00:25 | 58 |
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