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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Keypoint MoSeq Resource Report Resource Website 1+ mentions |
Keypoint MoSeq (RRID:SCR_025032) | source code, software resource | Software application as machine learning-based platform for identifying behavioral modules from keypoint data without human supervision. Package provides tools for fitting MoSeq model to keypoint tracking data. Used to infer pose dynamics with keypoint data in addition to behavioral syllables. | OpenBehavior, infer pose dynamics, keypoint data, identifying behavioral modules, keypoint tracking data, parsing behavior, linking point tracking to pose dynamics, | has parent organization: Harvard University; Cambridge; United States | NIA RF1AG073625; NINDS R01NS114020; NINDS U24NS109520; Simons Foundation Autism Research Initiative ; Simons Collaboration on Plasticity and the Aging Brain ; NINDS U19NS113201; Simons Collaboration on the Global Brain ; NINDS F31NS113385; NINDS F31NS122155; Alfred P. Sloan Foundation ; Salk Collaboration Grant |
DOI:10.1101/2023.03.16.532307 | Free, Available for download, Freely available | SCR_025032 | 2026-02-15 09:23:42 | 9 | ||||||||
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Diffusion-Model Resource Report Resource Website |
Diffusion-Model (RRID:SCR_027942) | source code, software resource | Software code for simulating diffusion in brain extracellular space images. | simulating diffusion, brain, extracellular space, images | Spanish Government ; NINDS R01NS130759; NSF |
PMID:41279667 | Free, Available for download, Freely available | SCR_027942 | , Diffusion Flux, DifFlux, Diffusion Flux Model | 2026-02-15 09:24:19 | 0 | ||||||||
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Lab Streaming Layer Resource Report Resource Website 50+ mentions |
Lab Streaming Layer (RRID:SCR_017631) | LSL | software application, software resource | System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. | Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG | has parent organization: University of California at San Diego; California; USA | Army Research Laboratory ; NINDS R01 NS047293 |
Free, Freely available | SCR_017631 | Lab Streaming Layer | 2026-02-15 09:22:04 | 67 | |||||||
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Diffusion MRI of Traumatic Brain Injury Resource Report Resource Website |
Diffusion MRI of Traumatic Brain Injury (RRID:SCR_001637) | Diffusion MRI of TBI | data or information resource, topical portal, portal | Project to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate composition or orchestration of workflows composed of different analysis and processing tasks (for example using LONI or XNAT pipelines) with the ultimate goal of providing automated no-click evaluations of diffusion MRI data. # Tool development: The final aspect of this project aims to facilitate and encourage tool development and contribution. By providing access to open datasets, they will create a platform on which tool developers can compare and improve and their tools. When tools are sufficiently mature they can be exposed in the infrastructure mentioned above and used by researchers and other developers. | diffusion tensor imaging, diffusion mri, standard specification, image repository, analysis, visualization, data sharing, common data element, service resource, data set |
is related to: vIST/e is related to: Camino is related to: DTI and Fibertools Software Package is related to: Diffusion Tensor Imaging ToolKit is related to: ExploreDTI is related to: Connectome Mapping Toolkit is related to: TORTOISE is related to: MITK Diffusion is related to: MRtrix is related to: MIPAV: Medical Image Processing and Visualization is related to: DTI Blog is related to: FSL has parent organization: University of Chicago; Illinois; USA |
Traumatic brain injury | NINDS | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153906 | SCR_001637 | 2026-02-16 09:45:32 | 0 | ||||||
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Rat Genome Database: Neurological Disease Portal Resource Report Resource Website 10+ mentions |
Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) | data or information resource, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools. | gene, analysis, biological, data, database, disease, genome, model, neurological, neuroscience, pathway, phenotype, qtl, rat, research | has parent organization: Medical College of Wisconsin; Wisconsin; USA | Neurological disease | RGD ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33773 | http://rgd.mcw.edu | SCR_008685 | RGD Neurological Disease Portal | 2026-02-16 09:47:14 | 14 | |||||
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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, storage service resource, data or information resource, service resource, software resource, software repository, portal, data repository | 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: PST 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: 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: 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: VIEWPixx lists: 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: 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 |
NIH Blueprint for Neuroscience Research ; NIMH ; NIDA ; NIBIB U24 EB023398; NINDS R44 NS074540 |
PMID:26044860 PMID:18999128 |
Free, Freely available | nif-0000-00202, r3d100010784 | https://doi.org/10.17616/R3W32N | SCR_003430 | 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 | 2026-02-17 10:00:17 | 338 | ||||
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NIH MRI Study of Normal Brain Development Resource Report Resource Website 1+ mentions |
NIH MRI Study of Normal Brain Development (RRID:SCR_003394) | Pediatric MRI Study | data or information resource, narrative resource, data set, experimental protocol | Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2. | young human, child, pediatric, experimental protocol, brain, brain development, development, mri, minc, clinical, behavior, anatomical mri, diffusion tensor imaging, mr spectroscopy, adolescent, clinical data, behavioral data, data visualization software, clinical measure, behavioral measure, physical neurological examination, behavioral rating, neuropsychological testing, structured psychiatric interview, hormonal measure, image collection, neonate, clinical neuroinformatics, dicom, minc2, magnetic resonance, nifti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: NIH Data Sharing Repositories is related to: NIH Data Sharing Repositories has parent organization: National Institutes of Health |
Healthy, Normal | NICHD ; NIDA ; NIMH ; NINDS ; NIH Blueprint for Neuroscience Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00201 | http://www.bic.mni.mcgill.ca/nihpd/info/, https://nihpd.crbs.ucsd.edu/nihpd/info/index.html | SCR_003394 | NIH Pediatric MRI Data Repository, Pediatric MRI Data Repository | 2026-02-17 10:00:16 | 6 | ||||
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NITRC-IR Resource Report Resource Website 1+ mentions |
NITRC-IR (RRID:SCR_004162) | NITRC IR | storage service resource, data or information resource, catalog, database, service resource, image database, data repository, image repository | Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data. | database, neuroimaging, magnetic resonance, mri, image collection, nifti, dicom |
uses: XNAT Central is used by: NIF Data Federation lists: 1000 Functional Connectomes Project lists: studyforrest.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 1000 Functional Connectomes Project is related to: NITRC Enhanced Services has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Bipolar Disorder, Schizophrenia, Parkinson's disease, ADHD | NINDS R44 NS074540; NIBIB U24 EB023398 |
PMID:26044860 | Free, Available for download, Freely available | nlx_18447, SCR_015623 | SCR_004162 | NeuroImaging Tools and Resources Collaboratory Image Repository, NITRC Image Repository | 2026-02-17 10:00:35 | 8 | ||||
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NIMH Data Archive Resource Report Resource Website 100+ mentions |
NIMH Data Archive (RRID:SCR_004434) | NDA | storage service resource, data or information resource, database, service resource, data repository | The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI). | afni brik, ascii, bshort, bfloat, connectome file format, cifti, clinical neuroinformatics, cor, dicom, imaging genomics, inc, minc2, nifti, os independent, philips par/rec, tex, vrml, phenotype, neuroimaging, genomic, gender, male, female, dti, fmri, mri, spectroscopy, eeg, microarray, snp, cnv, next-generation sequencing, gene regulation, gene expression, genotyping, pedigree, clinical assessment, FASEB list |
uses: HED Tags is used by: National Database for Clinical Trials related to Mental Illness is used by: RDoCdb is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: National Database for Clinical Trials related to Mental Illness is related to: RDoCdb has parent organization: National Institute of Mental Health hosts: GUID Tool |
Autism, Autism spectrum disorder, Asperger Syndrome, Normal control, Sibling control, Parental control, Fragile X syndrome | NIMH ; NINDS ; NIEHS ; NICHD ; Center for Information Technology |
Restricted | nlx_143735, r3d100010717, r3d100012653 | http://www.nitrc.org/projects/ndarportal https://data-archive.nimh.nih.gov/ https://doi.org/10.17616/R37K63 https://doi.org/10.17616/R3XV5P |
http://ndar.nih.gov/ | SCR_004434 | NDAR, National Database for Autism Research, National Institute of Mental Health Data Archive, National Database for Autism Research (NDAR) | 2026-02-17 10:00:31 | 291 | |||
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Repository of molecular brain neoplasia data Resource Report Resource Website 1+ mentions |
Repository of molecular brain neoplasia data (RRID:SCR_004704) | REMBRANDT | data or information resource, topical portal, production service resource, analysis service resource, database, service resource, data analysis service, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotype |
is related to: Gene Ontology is related to: Glioma Molecular Dignostic Initiatives has parent organization: National Cancer Institute |
Glioma, Brain cancer, Brain tumor | NCI ; NINDS |
PMID:19208739 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00230 | SCR_004704 | REMBRANDT (Repository of Molecular Brain Neoplasia Data), REMBRANDT - Repository of Molecular Brain Neoplasia Data, REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) | 2026-02-17 10:00:49 | 2 | ||||
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Computational Neuroanatomy Group Resource Report Resource Website |
Computational Neuroanatomy Group (RRID:SCR_007150) | CNG | data or information resource, topical portal, portal, software resource | Multidisciplinary research team devoted to the study of basic neuroscience with a specific interest in the description and generation of dendritic morphology, and in its effect on neuronal electrophysiology. In the long term, they seek to create large-scale, anatomically plausible neural networks to model entire portions of a mammalian brain (such as a hippocampal slice, or a cortical column). Achievements by the CNG include the development of software for the quantitative analysis of dendritic morphology, the implementation of computational models to simulate neuronal structure, and the synthesis of anatomically accurate, large scale neuronal assemblies in virtual reality. Based on biologically plausible rules and biophysical determinants, they have designed stochastic models that can generate realistic virtual neurons. Quantitative morphological analysis indicates that virtual neurons are statistically compatible with the real data that the model parameters are measured from. Virtual neurons can be generated within an appropriate anatomical context if a system level description of the surrounding tissue is included in the model. In order to simulate anatomically realistic neural networks, axons must be grown as well as dendrites. They have developed a navigation strategy for virtual axons in a voxel substrate. | dendritic morphology, neuronal morphology, neuronal electrophysiology, mammalian brain, neural network, cell, model, morphology, network connectivity, basal ganglia, modeling software, hippocampus, hermissenda learning, caulescence, tree structure, neuron, virtual neural network, morphological class of neuron, virtual neuron, virtual brain, ca3 pyramidal cell, arborvitae, ca1 pyramidal cell, polymorphic cell, dg granule cell, axonal navigation, synaptic connectivity, neuroplasticity, neuroanatomy, neuroinformatics, computation, network model, neural circuit, cellular event, expression, ca3, ca1 pyramidal neuron, digital morphological reconstruction, digital reconstruction, dendrite, axon, neuronal tree, signaling pathway |
has parent organization: George Mason University: Krasnow Institute for Advanced Study is parent organization of: L-Measure is parent organization of: Hippocampus 3D Model |
NINDS ; NIMH ; NSF ; Human Brain Project |
nif-0000-00503 | http://krasnow.gmu.edu/cn3/index3.html | SCR_007150 | Computational Neuroanatomy Group at the Krasnow Institute for Advanced Study | 2026-02-17 10:01:04 | 0 | ||||||
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BrainML Resource Report Resource Website |
BrainML (RRID:SCR_007087) | BrainML | narrative resource, storage service resource, data or information resource, database, service resource, standard specification, data repository |
Set of standards and practices for using XML to facilitate information exchange between user application software and neuroscience data repositories. It allows for common shared library routines to handle most of the data processing, but also supports use of structures specialized to the needs of particular neuroscience communities. This site also serves as a repository for BrainML models. (A BrainML model is an XML Schema and optional vocabulary files describing a data model for electronic representation of neuroscience data, including data types, formats, and controlled vocabulary. ) It focuses on layered definitions built over a common core in order to support community-driven extension. One such extension is provided by the new NIH-supported neuroinformatics initiative of the Society for Neuroscience, which supports the development of expert-derived terminology sets for several areas of neuroscience. Under a cooperative agreement, these term lists will be made available Open Source on this site. The repository function of this site includes the following features: * BrainML models are published in searchable, browsable form. * Registered users may submit new models or new versions of existing models to accommodate data of interest. * BrainML model schema and vocabulary files are made available at fixed URLs to allow software applications to reference them. * Users can check models and/or instance documents for correct format before submitting them using an online validation service. To complement the BrainML modeling language, a set of protocols have been developed for BrainML document exchange between repositories and clients, for indexing of repositories, and for data query. |
format, development, information, mechanism, metaformat, model, neuroinformatics, neuroscience, standard, terminology, validation, vocabulary, xml, data sharing, xml schema compact syntax, xml schema, interoperability, semantics |
is used by: Neurodatabase.org has parent organization: Weill Cornell Medical College; New York; USA |
Human Brain Project ; NIMH MH/NS57153; NINDS MH/NS57153 |
Public, The community can contribute to this resource | nif-0000-21070 | http://brainml.org | SCR_007087 | BrainML.org | 2026-02-17 10:01:10 | 0 | |||||
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ModelDB Resource Report Resource Website 100+ mentions |
ModelDB (RRID:SCR_007271) | ModelDB | storage service resource, data or information resource, database, service resource, data repository | Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions. | repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, data |
is used by: NIF Data Federation lists: ModelRun is listed by: 3DVC is listed by: Biositemaps is listed by: Integrated Models is related to: SimToolDB is related to: NeuronDB is related to: NeuronVisio is related to: Integrated Manually Extracted Annotation is related to: Allen Institute for Brain Science has parent organization: Yale University; Connecticut; USA works with: MicrocircuitDB |
NIMH ; NINDS ; NCI ; Human Brain Project ; NIDCD P01 DC004732; NIDCD R01 DC009977 |
PMID:15218350 PMID:15055399 PMID:8930855 |
Free, Freely available, Acknowledgement requested | nif-0000-00004, r3d100011330 | https://doi.org/10.17616/R3P61F | SCR_007271 | Model_DB, Model Database, Model DB, Model-DB | 2026-02-17 10:01:12 | 304 | ||||
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Cognitive and Emotional Health Project: The Healthy Brain Resource Report Resource Website |
Cognitive and Emotional Health Project: The Healthy Brain (RRID:SCR_007390) | CEHP | data or information resource, topical portal, portal, database | Trans-NIH project to assess the state of longitudinal and epidemiological research on demographic, social and biologic determinants of cognitive and emotional health in aging adults and the pathways by which cognitive and emotional health may reciprocally influence each other. A database of large scale longitudinal study relevant to healthy aging in 4 domains was created based on responses of investigators conducting these studies and is available for query. The four domains are: * Cognitive Health * Emotional Health * Demographic and Social Factors * Biomedical and Physiologic Factors | healthy aging, cognitive health, demographics, longitudinal study, aging study, late adult human, cognition, emotion, adult human, longitudinal, epidemiology, psychosocial, questionnaire, social factor, physiologic factor | has parent organization: National Institutes of Health | Cognitive impairment, Emotional disorder, Aging | NIA ; NIMH ; NINDS |
nif-0000-00421 | SCR_007390 | Cognitive and Emotional Health Project (CEHP), Cognitive Emotional Health Project: The Healthy Brain, Cognitive Emotional Health Project, Cognitive and Emotional Health Project | 2026-02-17 10:01:14 | 0 | ||||||
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National NeuroAIDS Tissue Consortium Resource Report Resource Website 10+ mentions |
National NeuroAIDS Tissue Consortium (RRID:SCR_007323) | NNTC | biomaterial supply resource, tissue bank, brain bank, material resource | Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators. | human immunodeficiency virus, nervous tissue, cerebral spinal fluid, blood, tissue, brain, neuromedical data, neuropsychiatric data, tissue, plasma, peripheral blood mononuclear cell, serum, urine, spinal cord, nervous tissue, pituitary gland, trigeminal ganglia, dorsal root ganglion, peripheral nerve, lymph node, liver, spleen, adipose tissue, bone marrow, muscle, hair, heart, thymus, kidney, lung, eye, brain, ante-mortem, post-mortem, normal, subsyndromic, minor cognitive motor disorder, hiv - associated dementia, cytomegalovirus encephalitis, neurological impairment, traumatic brain injury, neurocognitive disease, frozen, fixed, aids, one mind tbi, asymptomatic neurocognitive impairment, minor cognitive disorder, gene array, snp |
is listed by: One Mind Biospecimen Bank Listing is related to: Manhattan HIV Brain Bank is related to: CHARTER - CNS HIV Antiretroviral Therapy Effects Research |
Human immunodeficiency virus, Neurocognitive disease, Normal, Subsyndromic, Minor Cognitive Motor Disorder, HIV - Associated Dementia, Cytomegalovirus Encephalitis, Neurological impairment, Infectious disease | NIMH ; NINDS ; NIH Blueprint for Neuroscience Research |
Public: The NNTC encourages external researchers to submit tissue requests for ancillary studies. | nif-0000-00193 | SCR_007323 | nntc.org, nntc | 2026-02-17 10:01:05 | 11 | |||||
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Olfactory Receptor DataBase Resource Report Resource Website 1+ mentions |
Olfactory Receptor DataBase (RRID:SCR_007830) | ORDB | storage service resource, data or information resource, production service resource, analysis service resource, database, service resource, data analysis service, data repository | Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors. | fungal, pheromone receptor, gene, chemosensory, chemosensory receptor, g protein-coupled receptor, olfaction receptor, protein, receptor, taste papilla receptor, vomeronasal organ receptor, olfactory receptor, nucleotide, amino acid, chemoreceptor sequence, olfactory receptor sequence, chemoreceptor, sequence |
is used by: NIF Data Federation is listed by: 3DVC is related to: Odor Molecules DataBase is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
Aging | Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; National Aeronautics and Space Administration ; NIDCD RO1 DC 009977; NIDCD P01 DC 04732; NLM G08 LM05583 |
PMID:11752336 PMID:9847223 PMID:9218144 |
Public, Private, Acknowledgement requested, The community can contribute to this resource | nif-0000-03213 | SCR_007830 | Olfactory Receptors Database | 2026-02-17 10:01:17 | 4 | ||||
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NIH Pediatric MRI Data Repository Resource Report Resource Website |
NIH Pediatric MRI Data Repository (RRID:SCR_014149) | NIHPD | data or information resource, image collection, database | A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult. | database, image collection, structural mri, dti, spectroscopy, human brain, child |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
NICHD ; National Institute on Drug Abuse ; NIMH ; NINDS |
Available to the research community, Access must be granted | http://pediatricmri.nih.gov/nihpd/info/index.html | SCR_014149 | Pediatric MRI Data Repository, NIH MRI Study of Normal Brain Development Pediatric MRI Data Repository | 2026-02-17 10:02:31 | 0 | ||||||
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HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | data or information resource, narrative resource, standard specification | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Swartz Foundation ; Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293 |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-02-17 10:02:05 | 7 | |||||
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Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 Resource Report Resource Website |
Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 (RRID:SCR_014127) | 3d visualization software, software application, data processing software, software resource, data visualization software | A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers. | filter, data visualization software, 3d visualization, tractography, algorithm, fiber tracking, HARDI |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NINDS NS066340 | Available for download | http://www.cise.ufl.edu/~salehian/Softwares.html | SCR_014127 | IUKF Tractography Software v1.0, IUKF Tractography Software, Intrinsic Unscented Kalman Filter Tractography Software, Intrinsic Unscented Kalman Filter Tractography Software v1.0 | 2026-02-17 10:02:33 | 0 | |||||||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | narrative resource, data or information resource, catalog, database, service resource, standard specification, data set | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NHGRI U01 HG004597; NHGRI U41HG007050; NIDA ; OBSSR ; NIMH ; NHLBI ; NIMHD ; TRSP ; NHGRI U24 HG012556; ODP ; NINDS ; NCI |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-02-17 10:00:57 | 61 |
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