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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | analysis service resource, data access protocol, data analysis service, data or information resource, data repository, data set, image repository, production service resource, service resource, software resource, source code, storage service resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01 |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me, http://www.nitrc.org/projects/ocp/ | SCR_004232 | SciCrunch Registry | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-10-31 12:13:46 | 7 | ||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | collaboration tool, data management software, data processing software, software application, software resource | 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 | SciCrunch Registry | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-10-31 12:14:27 | 16 | |||||
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Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | data analysis software, data processing software, data visualization software, software application, software resource | Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. | MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: OpenMEEG is related to: Open MEG Archive is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
CNRS ; McGill University ; NIBIB R01 EB000473; NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB026299 |
PMID:21584256 | Free, Available for download, Freely available | nif-0000-10267 | http://www.nitrc.org/projects/bst, https://github.com/brainstorm-tools/brainstorm3 | SCR_001761 | SciCrunch Registry | brainstorm3 | 2026-10-31 12:12:56 | 622 | ||||
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3D Slicer Resource Report Resource Website 1000+ mentions |
3D Slicer (RRID:SCR_005619) | Slicer | data processing software, data visualization software, image analysis software, software application, 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 | SciCrunch Registry | Slicer, 3D Slicer: A multi-platform free and open source software package for visualization and medical image computing, 3D Slicer, 3DSlicer | 2026-10-31 12:14:17 | 3187 | |||||
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Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | data analysis software, data processing software, simulation software, software application, software resource | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | SciCrunch Registry | 2026-10-31 12:16:59 | 13 | |||||
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eConnectome Resource Report Resource Website 10+ mentions |
eConnectome (RRID:SCR_009618) | eConnectome | data processing software, image analysis software, image processing software, software application, software resource | An open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome La Sapienza. | eeg, meg, electrocorticography, forward - inverse, matlab, microsoft, modeling, multivariate analysis, region of interest, segmentation, statistical operation, visualization, windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIBIB RO1 EB006433; NIBIB RO1 EB007920 |
GNU General Public License | nlx_155844 | http://www.nitrc.org/projects/econnectome | SCR_009618 | SciCrunch Registry | Electrophysiological Connectome | 2026-10-31 12:15:00 | 31 | |||||
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SPM Anatomy Toolbox Resource Report Resource Website 100+ mentions |
SPM Anatomy Toolbox (RRID:SCR_013273) | SPM Anatomy Toolbox | software resource | A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space. | human, brain, imaging, functional magnetic resonance imaging, structure, mapping, atlas, pet, neuroimaging | is related to: SPM | NIMH ; NINDS ; NIBIB ; DFG KFO-112; DFG Schn 362/13-2 |
PMID:15850749 | nif-0000-10477 | SCR_013273 | SciCrunch Registry | 2026-10-31 12:15:53 | 108 | |||||||
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ITK-SNAP Resource Report Resource Website 1000+ mentions |
ITK-SNAP (RRID:SCR_002010) | data processing software, image analysis software, segmentation software, software application, software resource | Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). | medical, image, segmentation, delineating, anatomical, structure, region, MRI, CT, 3D image, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: neurodebian is related to: AHEAD is related to: LiverSegm is related to: Waxholm Space Atlas of the Sprague Dawley Rat Brain is related to: Waxholm Space has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB014346 | PMID:29946897 | Free, Available for download, Freely available | nif-0000-00317 | https://github.com/google/neuroglancer, https://opensource.google.com/projects/neuroglancer | SCR_002010 | SciCrunch Registry | 2026-10-31 12:13:00 | 2647 | ||||||
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Diffusion Tensor Imaging ToolKit Resource Report Resource Website 10+ mentions |
Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) | DTI-TK | data processing software, image analysis software, software application, software resource, software toolkit | A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation | dti, visualization, segmentation, resampling, smoothing, warping, registration, spatial normalization, atlas construction, analysis, atlas application, intersubject, image-to-template, analyze, nifti-1, macos, linux |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury is related to: Camino is related to: MRI Studio has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: SourceForge |
NIBIB 1R03EB009321-01 | Free, Available for download, Freely available | nlx_153914 | http://www.nitrc.org/projects/dtitk | SCR_001642 | SciCrunch Registry | 2026-10-31 12:12:54 | 25 | ||||||
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NeuroImaging Tools and Resources Collaboratory (NITRC) Resource Report Resource Website 100+ mentions |
NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430) | NITRC | community building portal, data or information resource, data repository, portal, service resource, software repository, software resource, storage service resource | Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource. | collaboration, information, resource, structural, functional, neuroimaging, MRI, fMRI, EEG, MEG, PET |
is used by: NIF Data Federation is used by: Consortium for Reliability and Reproducibility is used by: DataLad is recommended by: National Library of Medicine lists: Dipy lists: 3DMeshMetric lists: MPScope lists: VectorValuedHistogramNormalizer lists: Faceted Search Based Ontology Visualizer lists: Morphometry BIRN lists: Colin 3T/7T High-resolution Atlas lists: CMFreg lists: BrainFX lists: dinifti lists: Center for Computational Biology at UCLA lists: Convert MNI coordinates to or from XYZ lists: Licensing issues in software and data lists: Local Binary Pattern Analysis Tools for MR Brain Images lists: MIView lists: uManager lists: Penn Hippocampus Atlas lists: RapidArt lists: Scribe lists: ShapeWorks lists: Vervet Probabilistic Atlas lists: Talairach Daemon lists: ADHD-200 Preprocessed Data lists: LORIS - Longitudinal Online Research and Imaging System lists: NVM lists: Maps4Mipav (Exploratory JIST) lists: Autism Tissue Program lists: MEG Tools lists: PyNIfTI lists: LONI Visualization Tool lists: Mind Research Network - COINS lists: OpenElectrophy lists: CIFTI Connectivity File Format lists: 3DSlicerLupusLesionModule lists: BrainNetworkConstructionAnalysisPlatform lists: COMPARE lists: Data Format Tools lists: GesTr lists: I/OWA lists: MINC Example files lists: cbiNifti: Matlab/Octave Nifti library lists: BRAINSCut lists: C-PAC lists: Connectir lists: DicomBrowser lists: Hitachi Optical Topography System lists: Net Station API lists: imcalc: SPM batch image calculator lists: BRAINSCortex lists: Insight Segmentation and Registration Toolkit lists: LONI Debabeler lists: LONI Pipeline Processing Environment lists: NiLearn lists: MRI Studio lists: BraVa lists: Brede Wiki lists: Center for Functional Neuroimaging Technologies lists: Philips Users Community lists: medInria lists: Beijing: Eyes Open Eyes Closed Study lists: vIST/e lists: Camino lists: Diffusion Tensor Imaging ToolKit lists: TORTOISE lists: NIDAG: Neuroimaging Data Access Group lists: MRI CVPR lists: vuTools lists: Medical Image Processing and Visualization in Virtual Environments lists: Brainstorm lists: Atlas3D lists: FMRISTAT - A general statistical analysis for fMRI data lists: FreeSurfer lists: Rosetta Bit lists: Laboratory of Neuro Imaging lists: Group ICA of fMRI Toolbox lists: Hierarchical Attribute Matching Mechanism for Elastic Registration lists: Internet Brain Segmentation Repository lists: Neural ElectroMagnetic Ontologies (NEMO) Project lists: Wavelet-based Image Fusion lists: ITK-SNAP lists: Internet Brain Volume Database lists: Statistical non-Parametric Mapping lists: VoxBo lists: NITRC Computational Environment lists: Spatially Constrained Parcellation lists: Cluster reporter lists: Cluster Extent Correction lists: 4D Atlases Construction lists: CIGAL lists: CleanLine lists: Computational Morphometry Toolkit lists: Cognitive Paradigm Ontology lists: aBEAT lists: MR Connectome Automated Pipeline lists: International Neuroinformatics Coordinating Facility lists: Functional Regression Analysis of DTI Tract Statistics lists: MCIC lists: MGDM: Multi Geometric Deformable Model lists: MIAS Registration Toolkit lists: Medical Image Visualization and Analysis lists: Microstructural correlation toolbox lists: MisterI lists: MriWatcher lists: Multiple Correlation Function Tool lists: NITRC Community Conferences Workshops and Meetings lists: BRAINSFit lists: INCF Software Center lists: BrainVision Analyzer lists: COGNISION lists: DPARSF lists: GLIRT lists: MINC lists: Group Level Imputation of Statistic Maps lists: MRIcron lists: Inter-Group Registration Toolbox lists: MCML and CONV lists: MEGSIM lists: MIRIAD lists: MRI Defacer lists: MS lesion segmentation challenge 2008 lists: Measure Projection Toolbox lists: Mindboggle lists: Mindboggle-101 atlases lists: ModelGUI lists: Multi-Modal MRI Reproducibility Resource lists: MultiTracer lists: Multicomponent T2 estimation with stimulated echo correction lists: NCANDA: Data Integration Component lists: NFT lists: Net Station EEG Software lists: Network Based Statistic Toolbox lists: NeuroScope lists: Numerical Fibre Generator lists: PSTNet: MRI Simulator lists: cortex lists: iBEAT lists: M3 lists: Group ICA Of EEG Toolbox lists: 4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration lists: Automatic Segmentation Tool Adapter lists: DTI-TEMPLATE-RHESUS-MACAQUES lists: LONI Provenance Editor lists: MNI N3 lists: MRI Digital Projection System lists: NIDB - Neuroinformatics Database lists: NIPY lists: NIRAL Utilities lists: NIRx NIRS Neuroimaging lists: NIRx2nirs: A NIRx to .nirs data converter lists: NITRC Enhanced Services lists: NITRC GForge Extensions lists: NPTK lists: NeuroImaging Analysis Kit (NIAK) lists: NiBabel lists: NiftyRec lists: Nipype lists: Nirfast lists: Nitime lists: Non-Rigid Image Registration Evaluation Project lists: Normative Independent Component Analysis lists: OEI: fMRI compatible olfactometer lists: ORS Visual SI lists: OpenMEEG lists: PANDA lists: PESTICA fMRI Physio Detection/Correction lists: PHYCAA+: adaptive physiological noise correction for BOLD fMRI lists: ParaView lists: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) lists: Presentation lists: PySurfer lists: Pythagorean Displacement and Motion Regressors lists: Quantitative Diffusion Tools lists: R-package for adaptive DWI analysis lists: R-package for adaptive fMRI analysis lists: REX lists: RFT FDR lists: ROBEX lists: RT Image lists: Resource Ontology Discussion Group lists: Rodent Brain Extraction Tool lists: Rodent Cortical Thickness Analysis lists: S-rep Fitting Statistics and Segmentation lists: SCIRun lists: SCRalyze lists: SOCK lists: SPHARM-MAT lists: SPHARM-PDM Toolbox lists: SRI24 Atlas: Normal Adult Brain Anatomy lists: Seg3D lists: ShapeComplexAtlas lists: Signed Differential Mapping lists: Sleuth lists: Slice:Drop lists: Slicer3 Example Modules lists: Source Information Flow Toolbox lists: Spanish Resting State Network lists: Spatial Analysis 3D lists: Stereoscopic Atlas of Intrinsic Brain Networks lists: UNC Infant 0-1-2 Atlases lists: UNC Primate Brain Atlas lists: XCEDE Schema lists: peak nii lists: pydicom lists: pyxnat lists: scikit-learn lists: shapeAnalysisMANCOVA - SPHARM tools lists: VMTK in 3D Slicer lists: 3D Interactive Chemical Shift Imaging lists: BRAINSSurfaceStats lists: Brain lesion segmentation tool using SVM lists: Diffusion Tractography with Kalman Filter lists: Fast Nonlocal Means for MRI denoising lists: Monte Carlo Simulation Software: tMCimg lists: Web Interfaces for Multiscale Images lists: STAPLE lists: Segmentation Validation Engine lists: Spatial Statistical Parametric Mapping lists: SpineSegmentation module for 3DSlicer lists: Stochastic Tractography System lists: Subject Library lists: TAPIR lists: TARQUIN lists: Template Image Processing Library lists: TetraMetrix lists: TractoR: Tractography with R lists: Triangle BioSystems lists: TumorSim lists: TurtleSeg lists: UNC Human Brain Atlas lists: VR Worlds 2 lists: Vaa3D lists: ValMap: simple statistical mapping tool lists: WFU Biological Parametric Mapping Toolbox lists: WFU Pipeline lists: Working Memory Trainer lists: vis: SPM Visualized Statistics toolbox lists: Synchronized Histological Image Viewing Architecture lists: LONI ShapeViewer lists: LONI ShapeTools lists: FFT Library lists: Automated recognition of brain region mentions in neuroscience literature. lists: NUTMEG lists: Cognitive Atlas lists: Mouse BIRN Atlasing Toolkit lists: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat lists: FSL lists: LEAD-DBS lists: Brainscape lists: EONS lists: BioImage Suite lists: ADNI - Alzheimer's Disease Neuroimaging Initiative lists: MindSeer lists: XNAT - The Extensible Neuroimaging Archive Toolkit lists: brainmap.org lists: ImageJ lists: Neuroimaging Informatics Technology Initiative lists: IMOD lists: Statistics Online Computational Resource lists: signalml.org lists: Mouse Biomedical Informatics Research Network lists: NIH MRI Study of Normal Brain Development lists: MGH-USC Human Connectome Project lists: Fusion ICA Toolbox lists: Corpus Callosum Thickness Profile Analysis Pipeline lists: ABIDE lists: Mouse Connectome Project lists: NITRC-IR lists: Open Connectome Project lists: neurodebian lists: NIMH Data Archive lists: ANTS - Advanced Normalization ToolS lists: XNAT Extras lists: TrackVis lists: Brain Connectivity Toolbox lists: FieldTrip lists: LONI Inspector lists: BrainLiner lists: OpenNeuro lists: Biomedical Informatics Research Network lists: McConnell Brain Imaging Center MNI Macaque Atlas lists: SINOMO lists: DONE: Detection of Outlier NEurons lists: Neuro Bureau lists: ADHD-200 Sample lists: 1000 Functional Connectomes Project lists: PubBrain lists: CBRAIN lists: ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis lists: Bisque lists: 3D Slicer lists: Internet Analysis Tools Registry lists: Neuromorphometrics lists: Analysis of Functional NeuroImages lists: Automated Image Registration lists: BASH4RfMRI lists: MNE software lists: Object-Oriented Development Interface for NMR lists: NYU CSC TestRetest lists: Optseq - fMRI Event Scheduler lists: TOADS-CRUISE Brain Segmentation Tools lists: MouseTracker lists: Hammer And WML Modules for 3D Slicer lists: ABC (Atlas Based Classification) lists: Allen Brain Atlas API lists: Viking Viewer for Connectomics lists: ARCTIC lists: ArtRepair for robust fMRI lists: Automatic Registration Toolbox lists: Artifact Detection Tools lists: Segmentation of Hippocampus Subfields lists: ASL data processing tool box lists: Bioelectromagnetism Matlab Toolbox lists: PyMVPA lists: Human Imaging Database lists: BrainImage Software lists: Brede Toolbox lists: Computerized Anatomical Reconstruction and Editing Toolkit lists: BrainColor: Collaborative Open Labeling Online Resource lists: Registry Builder Data Harmonization and Aggregation Tool lists: PsychoPy lists: NiftySim lists: NiftyReg lists: Neurobiological Image Management System lists: BRAINSTools lists: MeshValmet: Validation Metric for Meshes lists: BrainSuite lists: DW-MRI Random Walk Simulator lists: Web Game for Collaborative Labeling lists: BrainVoyager Brain Tutor lists: POLGUI - Matlab Polhemus Interface lists: BrainVoyager Brain Viewer lists: NeuroPub Visualizer lists: NODDI Matlab Toolbox lists: MITK Diffusion lists: Federal Interagency Traumatic Brain Injury Research Informatics System lists: BrainMaps.org lists: PRoNTo lists: Scalable Brain Atlas lists: NIH Human Connectome Project lists: Mesh-based Monte Carlo (MMC) lists: Matlab Neuroshare Library lists: MRtrix lists: MABMIS: Multi-Atlas Based Multi-Image Segmentation lists: Monte Carlo eXtreme lists: Whole Brain Catalog lists: BCILAB lists: ABSORB: Atlas Building by Self-Organized Registration and Bundling lists: VAMCA lists: SPM lists: Low Resolution Electromagnetic Tomography lists: SurfStat lists: Cambridge Brain Activation lists: CLEAVE lists: CoCoMac lists: fMRI Data Center lists: Function BIRN lists: EEGLAB lists: BrainVISA / Anatomist lists: MIPAV: Medical Image Processing and Visualization lists: NeuroLens lists: WFU PickAtlas lists: Open Access Series of Imaging Studies lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis lists: xjView: A Viewing Program For SPM lists: Human Connectome Coordination Facility lists: ASL spm8 lists: Integrated Manually Extracted Annotation lists: JIST: Java Image Science Toolkit lists: Functional Analysis of Diffusion Tensor lists: AHEAD lists: ANTsR lists: 3DBar lists: Cancer Imaging Archive (TCIA) lists: Pediatric Imaging Neurocognition and Genetics lists: Atlasing of the basal ganglia lists: cmrep lists: 3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood lists: AutoSeg lists: BXH/XCEDE Tools lists: Baby Brain Toolkit lists: Best Practices for Software Development lists: Brain Catalogue lists: Draw3D and Meshinator lists: Brain Segmentation Testing Protocol lists: BrainNet Viewer lists: BrainSolution lists: Brainvox lists: C8: Corpus Callosum Computations lists: CAMINO-TRACKVIS lists: CANDI Share: Schizophrenia Bulletin 2008 lists: CBS High-Res Brain Processing Tools lists: CCSeg - Corpus Callosum Segmentation lists: Cerebral Blood Flow Database and Analysis Pipeline lists: Create DWI Atlas lists: DFBIdb lists: DIAMOND lists: DICOM UploadGUI lists: DOTS WM tract segmentation lists: DTI Fiber Tract Statistics lists: DW-MRI registration in FSL lists: DbGaP Cleaner lists: DentalTools lists: Diffusion MRI - In-vivo and Phantom Data lists: Diffusion MRI at DKFZ Heidelberg lists: Diffusion Warp lists: Disease State Prediction lists: EEG human categorization data lists: Epsilon Radial Networks lists: FBIRN Image Processing Scripts lists: FSL extensions lists: False Discovery Rate Weighted lists: Fiber Tracking Tool lists: Fiber-tracking based on Finsler distance lists: FiberViewerLight lists: Finsler tractography module for Slicer lists: Fluid Registration and Atlas Toolkit lists: Framework for Open Programmatic Access lists: Functional Connectivity Community lists: Functional ROI Atlas lists: Functional and Structural Neuroimaging Journals Listing lists: GAMBIT lists: GAMMA lists: BRAINSMush lists: GPU based affine registration lists: GRETNA lists: Generalized Covariance Analysis lists: Generalized PPI Toolbox lists: Group Information Guided ICA lists: Groupwise Image Registration Toolbox lists: HD Neuro-Informatics lists: Hitachi2nirs lists: IDeA Lab brain image processing suite lists: INCF Neuroimaging Data Sharing lists: INIA19 Primate Brain Atlas lists: JHU Proj. in Applied Medical Imaging lists: JIST Resources for Algorithm Development lists: BRAINSROIAuto lists: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI lists: Landman NeuroImaging Tools lists: Local Label Learning Segmentation lists: MASI Label Fusion lists: MASIMatlab lists: MATLAB Tutorial on Diffusion Tensor MRI lists: Multi-Echo Independent Component Regression Group-Level Connectivity Dataset lists: Multi-fiber Reconstruction from DW-MRI lists: NITRC Books lists: Network Modification Tool Lite lists: Non-rigid groupwise registration method lists: Rockland Download Link Script lists: Subject Order-Independent Group ICA lists: Task Independent Fluctuations Discussion lists: UNC Human DTI Brain Atlas lists: BRAINSTestData lists: cPPI Toolbox for fMRI lists: fMRI Classification in R lists: fMRI-CPCA lists: fNIRS Data Analysis Environment lists: factory t1 dti lists: BRAINSDemonWarp lists: AMILab lists: ADJUST lists: ALVIN lists: Age Related Atrophy Dataset lists: B0 and eddy current correction for DTI lists: BESA lists: BSMac lists: BVQXtools lists: BioMesh3D lists: BrainBrowser lists: BrainGraph Editor lists: BrainMagix SPM Viewer lists: BrainMask Volume Processing Tool lists: Brainsight lists: Brainwaver lists: CANDI Neuroimaging Access Point lists: CBFBIRN lists: CDF-HC PointSetReg lists: GIMIAS lists: CURRY lists: CalaTK lists: CoCoMac-Paxinos3D viewer lists: INVIZIAN lists: CONN lists: Connectome File Format lists: Connectome Viewer lists: Cytoseg lists: DICCCOL predictor lists: DRAMMS lists: DSI Studio lists: Level-set Segmentation for Slicer3 lists: DTI BrainImageScope lists: DTI-Reg lists: DTIProcess ToolKit lists: DWI/DTI Quality Control Tool: DTIPrep lists: Diffusional Kurtosis Estimator lists: Distributome lists: ImageVis3D lists: E-Prime lists: E-Prime Extensions for fMRI lists: EEGVIS lists: EEProbe lists: EMSE Suite lists: LONI Brain Parser lists: EPILAB lists: ERPLAB lists: FIV lists: FMRIpower lists: Fiber Optic Button Response System lists: Free-D lists: GIFTI lists: GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data lists: HAMMER Suite lists: HERMES lists: HI-SPEED Software Packets lists: Homer2 lists: IIT Human Brain Atlas lists: JIP Analysis Toolkit lists: Jim lists: LDDMM lists: LIBEEP lists: LIMO EEG lists: LONI De-identification Debablet lists: Waxholm Space lists: Lipsia lists: Lumina LP- 400 Response System lists: MRI Dataset for Hippocampus Segmentation lists: MaCH-Admix lists: Mach2dat lists: Mag Design and Engineering lists: MagVenture: MagPro Magnetic Stimulator lists: SR Research EyeLink Eye Trackers lists: Mango lists: Manually Labeled MRI Brain Scan Database lists: MarsBaR region of interest toolbox for SPM lists: MazeSuite lists: MoTrak Head Motion Tracking System lists: NCIGT Fast Imaging Library lists: NeuroWeb - NeuroImaging Database lists: Neuroimaging Made Easy Blog lists: Neurophysiological Biomarker Toolbox lists: SVV lists: Slicer3 Module Rician noise filter lists: UNC/Utah NAMIC DTI Fiber Analysis Framework lists: caGWAS lists: eConnectome lists: elastix lists: fMRI Artefact rejection and Sleep Scoring Toolbox lists: MACH lists: fMRI Grocer lists: fNIR Devices lists: fanDTasia Java Applet: DT-MRI Processing lists: g.BSanalyze lists: iTools lists: iView X MRI-LR - Eye Tracking for fMRI lists: map3d lists: NICE-SIGN lists: NIRS-SPM lists: NITRC Community lists: NordicNeuroLab lists: PICSL Multi-Atlas Segmentation Tool lists: Paradigm lists: Pipeline Neuroimaging VirtualEnvironment lists: Pipeline System for Octave and Matlab lists: ProbabilisticBiasCorrection lists: Program for optimal design of blocked fMRI experiments lists: QCQP lists: REST: a toolkit for resting-state fMRI lists: Robust Biological Parametric Mapping lists: SPM SS - fMRI functional localizers lists: Solar Eclipse Imaging Genetics tools lists: VPixx: VIEWPixx /3D lists: resting-state pediatric imaging template lists: DATAPixx lists: GTRACT lists: Wisconsin White Matter Hyperintensities Segmentation Toolbox lists: COBRE lists: AngioCalc Cerebral Aneurysm Calculator lists: USC Multimodal Connectivity Database lists: BRAINSConstellationDetector lists: ASA - Advanced Source Analysis lists: BRAINSTracer lists: EYE-EEG (combined eye-tracking & EEG) lists: BrainVoyager lists: Mean Machine lists: ERP PCA Toolkit lists: LiverSegm lists: GSA-SNP lists: FastICA lists: DTI Atlas Builder lists: Neuroimaging in Python lists: Brain Decoder Toolbox lists: iso2mesh lists: CUDA-SPHERE-FWD-MEEG lists: BrainCSI lists: BrainVisa Morphology extensions lists: VPixx: VIEWPixx lists: VPixx: PROPixx lists: GenGen lists: MACH 1.0 lists: PennCNV lists: SumsDB lists: Integrated Software lists: NeuroLex lists: Parkinson's Progression Markers Initiative lists: NeuroSynth lists: Textpresso lists: ANNOVAR lists: Graphtools lists: Grantees Meeting for NITRC lists: FP-CIT SPECT brain template in MNI space lists: Brain Computer Interface 2000 Software Package lists: BEAST lists: Brian Simulator lists: Connectome Workbench lists: ConnectomeDB lists: DIAN - Dominantly Inherited Alzheimer Network lists: NKI-RS Enhanced Sample lists: EPILEPSIE database lists: GEneral NEural SImulation System: The Neurospaces Project lists: Hippocampome.org lists: Kitware lists: Kymata Atlas lists: L-Measure lists: MDR lists: neuroConstruct lists: Neurolucida lists: NeuroMorpho.Org lists: NEURON lists: NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification lists: NeuroVault lists: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) lists: NINDS Repository lists: NKI/Rockland Sample lists: ODIN lists: OBART lists: Open Science Framework lists: PLINK lists: MBF BioScience: Stereo Investigator lists: studyforrest.org lists: Virtual brain lists: TREES toolbox lists: APERTURE lists: 3dsvm lists: 7T Structural MRI scans ATAG lists: Atlases of amygdala and hippocampus for pediatric populations lists: BetA-Series COrrelation lists: bic-mni-models lists: BiofilmQuant lists: Biomag Discussion Group on Yahoo lists: Brain Entropy in space and time (BEst) lists: Brainnetome Atlas Viewer lists: Brainnetome fMRI toolkit lists: BROCCOLI lists: C-MIND Database lists: CARLsim: a GPU-accelerated SNN Simulator lists: Clinical Toolbox for SPM lists: CMIND PY lists: COST lists: dcm2nii lists: DICOMConvert lists: Displacement Field Viewer lists: DTI denoising lists: Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) lists: Efficient Permutation Testing lists: DTI-TK lists: ERPwavelab lists: ExPosition Packages lists: Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation lists: Forward: Accurate finite element electromagnetic head models lists: freesurfR lists: Functional Connectivity Analysis Tool for near-infrared spectroscopy data lists: GazeReader lists: gCCA lists: Generation R Pediatric MRI Resources lists: GIMME lists: GLMdenoise: a fast, automated technique for denoising task-based fMRI data lists: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity lists: HAMMER: Deformable Registration lists: HBM Hackathon lists: HDBIG lists: High-quality diffusion-weighted imaging of Parkinsons disease lists: MGA - Multimodal Glioma Analysis lists: Image Synthesis Tools lists: Imeka Tractography Service lists: International Imaging Genetics Conference lists: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 lists: Iterative dual-regression with sparse prior lists: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI lists: KWScene: MRML-based Atlas and Scene Builder/Reader/Writer lists: L-Neuron lists: Laplace Beltrami Filter on QuadEdge Meshes lists: libSBML lists: Lightweight Data Pipeline lists: Longitudinal MS Lesion Imaging Archive lists: MARS (Multi-Atlas Robust Segmentation) lists: minc-toolkit lists: minc-toolkit-testsuite lists: MISST - Microstructure Imaging Sequence Simulation ToolBox lists: MRI Neuroanatomy Labeling Services lists: MRIcroS lists: Multivariate General Linear Models (MGLM) on Riemannian Manifolds lists: Neoseg lists: NeoSegPipeline lists: NeuriteTracer lists: NeuroElf lists: Neuron-C lists: NIH Pediatric MRI Data Repository lists: NIH-CIDI Lung Segmentation Tool lists: NiiStat lists: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) lists: Notion ResearchPACS lists: NTU-DSI-122: a DSI template in ICBM-152 space lists: OpenViBE lists: OpenWalnut lists: Orientation Distribution Function in Constant Solid Angle (CSA-ODF) lists: Parkinsons Disease Discovery Database lists: Prediction and Diagnosis for Depression and Schizophrenia lists: Preprocessed Connectomes Project lists: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data lists: Ruby NIfTI lists: SCORE lists: SFMProject lists: ShapePopulationViewer lists: Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations lists: SPIKECOR: fMRI tool for automated correction of head motion spikes lists: Spinal Cord Toolbox lists: Stark Cross-Sectional Aging lists: Brain Coactivation Map lists: Multiscale Object Orientation Simulation Environment lists: Striatal Subregional VOImap lists: Topographica lists: Turbo-BrainVoyager lists: CRL Unbiased and Deformable Spatiotemporal Atlas of the Fetal Brain lists: UNC-Wisconsin Neurodevelopment Rhesus MRI Database lists: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) lists: VMTK in 3D Slicer lists: Wisconsin Cortical Thickness Analysis (CTA) Toolbox lists: XFSL: An FSL toolbox lists: XNBC lists: YMDTI: Diffusion Tensor Images of Healthy Young Males lists: BraTumIA (Brain Tumor Image Analysis) lists: CAWorks lists: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) lists: Graph Theory GLM (GTG) MATLAB Toolbox lists: Functional Mixed Processes Models lists: Papaya lists: Parallel Stochastic Ion Channel Simulator lists: Advanced Connectivity Analysis (ACA) lists: International Imaging Genetics Conference lists: Analyze Software System lists: Optseq lists: ENIGMA-DTI Pipeline lists: Umea Brain Arteries lists: MetaSearch lists: BrainBox lists: BluePyOpt lists: MultiXplore lists: Automatic Tractography-based Parcellation Pipeline lists: Epilepsy T1 and Hippocampal Segmentation Datasets lists: Mixed Effect Model of Genetic-Set and Environment Interaction lists: masked ICA (mICA) Toolbox lists: Altered States Database lists: User Friendly Functional Connectivity - UF²C lists: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open lists: Region to Region lists: Waxholm Space Atlas of the Sprague Dawley Rat Brain lists: Nutil - Neuroimaging utilities lists: MeshView lists: vini: A viewer for fMRI data lists: brainGraph lists: Diffusion Toolkit lists: Neurodocker lists: HeuDiConv: a heuristic-centric DICOM converter lists: Knowing what you know (kwyk) - Bayesian Brain Parcellation lists: Rhesus Macaque Brain Atlases lists: MIITRA atlas lists: MonkeyCBP lists: ReproNim/containers lists: ReproMan lists: ABCD-ReproNim Course lists: Ventricular Morphometry Analysis System lists: ONPRC18 Multimodal MRI Atlas lists: volBrain lists: Waxholm Space is affiliated with: Manual Align RTS2000 is related to: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: Harvard University; Cambridge; United States has parent organization: NIH Blueprint for Neuroscience Research is parent organization of: Licensing issues in software and data is parent organization of: NITRC Enhanced Services is parent organization of: Resource Ontology Discussion Group is parent organization of: NITRC-IR is parent organization of: 1000 Functional Connectomes Project is parent organization of: NYU CSC TestRetest is parent organization of: NITRC Books is parent organization of: NITRC Community is parent organization of: ABIDE is parent organization of: COBRE is parent organization of: Group Sparse Canonical Correlation Analysis is parent organization of: Challenge Competitions Collection is parent organization of: 1000 Functional Connectomes Project |
NIBIB U24 EB023398; NIDA ; NIH Blueprint for Neuroscience Research ; NIMH ; NINDS R44 NS074540 |
PMID:26044860 PMID:18999128 |
Free, Freely available | nif-0000-00202, r3d100010784, r3d100011515 | https://doi.org/10.17616/R3W32N | SCR_003430 | SciCrunch Registry | Neuroimaging Informatics Tools and Resources Clearinghouse, , NeuroImaging Tools and Resources Collaboratory, Neuroimaging Informatics Tools Resources Clearinghouse, NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse, NITRC - Neuroimaging Informatics Tools Resources Clearinghouse | 2026-10-31 12:13:25 | 374 |
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