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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-02-14 02:02:28 | 107 | |||||||
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BraVa Resource Report Resource Website 1+ mentions |
BraVa (RRID:SCR_001407) | BraVa | data or information resource, database | A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs). | digital reconstruction, morphometric analysis, cerebrum, arterial vasculature, magnetic resonance angiography, adult human, morphology, artery, arborization, circle of willis, cerebral artery, male, female, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Bravissima has parent organization: George Mason University: Krasnow Institute for Advanced Study |
Healthy | NINDS NS39600; NIBIB EB001955; NINDS NS061770; NIMH P20 MH52176 |
PMID:23727319 | Free, Freely Available | nlx_152630 | http://www.nitrc.org/projects/breva | SCR_001407 | 2026-02-14 02:06:04 | 8 | ||||
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BAMS Cells Resource Report Resource Website 10+ mentions |
BAMS Cells (RRID:SCR_003531) | BAMS Cells, BAMS Cell | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein. | neuroanatomy, cell, neuron, neural circuitry, brain |
is used by: NIF Data Federation has parent organization: Brain Architecture Management System |
NIMH ; NINDS ; NIBIB |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-90175 | http://brancusi.usc.edu/bkms/ | SCR_003531 | Brain Architecture Management System Cells | 2026-02-14 02:05:50 | 11 | |||||
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Richard M. Lucas Center for Imaging Resource Report Resource Website 1+ mentions |
Richard M. Lucas Center for Imaging (RRID:SCR_001406) | Lucas Center, CAMRT | biomedical technology research center, training resource | Biomedical technology research center that develops innovative technologies in five core research areas of magnetic resonance imaging and spectroscopy (MRI/MRS): # image reconstruction, fast imaging and radiofrequency (RF) pulse design methods, # R hardware development, # body imaging methods, # neuroimaging methods. # MR spectroscopy methods. In each of these areas, they capitalize on the long-standing, successful partnership and extensive experience in Stanford's Radiology and Electrical Engineering departments to improve and expand imaging technology for use in basic research and clinical care, and to provide cutting edge opportunities to the extramural community for biomedical research with MRI. Over its more than 18 years of existence, CAMRT has been motivated by and has served a wide base of extramurally sponsored collaborators and service users from leading medical and research institutions. Examples of collaborative projects are the development of real-time functional MRI biofeedback methods for neuroscience and clinical applications such as pain remediation, development of methods to mitigate metal artifacts in musculoskeletal imaging, development of novel RF pulses for many applications, and studies of breast cancer with efficient MRS methods. | magnetic resonance imaging, spectroscopy, x-ray imaging, ct imaging, imaging, neuroimaging | has parent organization: Stanford University School of Medicine; California; USA | Brain disorder, Cancer, Stroke, Heart disease | NIBIB | Free, Freely Available | nlx_152629 | http://med.stanford.edu/rsl/about/lucas.html | SCR_001406 | Lucas Center for Imaging, Center for Advanced Magnetic Resonance Technology | 2026-02-14 02:07:27 | 1 | ||||
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National Resource for Imaging Mass Spectrometry Resource Report Resource Website 1+ mentions |
National Resource for Imaging Mass Spectrometry (RRID:SCR_001416) | NRIMS | biomedical technology research center, training resource | Biomedical technology research center with the focus on the application to biomedical research of a new generation of secondary ion mass spectrometer (SIMS), the Multi-Isotope Imaging Mass Spectrometer (MIMS). MIMS is an ion microscope and an ion counter. MIMS provides high mass separation at high transmission (M/lambdaM > 10,000), high spatial resolution (< 40 nm) and has the unique capability of simultaneously recording several atomic mass images. Of the utmost importance, MIMS makes it possible for the first time (and at the intracellular level) to simultaneously image the distribution and measure the accumulation of molecules labeled with any isotopes, in particular with stable isotopes, for example with 15N. Thus, MIMS allows one to study localization, accumulation and turnover of proteins, fats, sugars and foreign molecules in cellular microdomains, donor-receiver cellular trafficking, stem cell nesting and localization of drugs. Their aim is to be a technological, methodological, and intellectual resource for researchers from a variety of disciplines. They seek to explore and develop the unique capabilities of MIMS and to bring cutting-edge information to biology and medicine that is currently unobtainable using existing technologies. | mass spectrometer, mass spectrometery, ion microscope, ion counter, imaging, ion, molecule | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41 EB001974-13 | nlx_152638 | SCR_001416 | 2026-02-14 02:07:48 | 7 | ||||||||
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NITRC GForge Extensions Resource Report Resource Website 1+ mentions |
NITRC GForge Extensions (RRID:SCR_002495) | software resource, software repository | Software repository of custom extensions to the GForge collaborative environment. | custom extension, gforge collaborative environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIBIB N02-EB-6-4281 | PMID:18999128 | Free, Available for download, Freely available | nlx_155891 | SCR_002495 | 2026-02-14 02:06:42 | 1 | |||||||
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Southwestern NMR Center for In Vivo Metabolism Resource Report Resource Website 1+ mentions |
Southwestern NMR Center for In Vivo Metabolism (RRID:SCR_001429) | Southwestern NMR Center | biomedical technology research center, training resource | Biomedical technology research center that develops and applies new methods for analysis of metabolic networks in intact tissues, animals and human patients. The importance of understanding abnormal metabolism in common diseases such as cancer, diabetes and heart disease has long been appreciated. Because of constraints in technology, however, much of this research has been conducted in isolated systems where clinical relevance may be uncertain. Progress in magnetic resonance technology provides a foundation for major advances towards new ways of imaging metabolism in patients. These new techniques offer the advantage of imaging biochemical pathways without radiation. The focus of this Resource is to bring these technologies to a level where clinical research is feasible through the development of new MR contrast agents, NMR spectroscopy at high fields, and imaging of hyperpolarized 13C. | metabolic network, tissue, imaging, metabolism, nuclear magnetic resonance, magnetic resonance, nuclear magnetic resonance spectroscopy | has parent organization: University of Texas Southwestern Medical Center; Texas; USA | Cancer, Diabetes, Heart disease | NIBIB 5P41EB015908-28 | Free, Freely Available | nlx_152653 | SCR_001429 | Southwestern NMR Center for in vivo Metabolism - NIBIB | 2026-02-14 02:07:27 | 1 | |||||
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EEG Motor Movement/Imagery Dataset Resource Report Resource Website 1+ mentions |
EEG Motor Movement/Imagery Dataset (RRID:SCR_004858) | EEG Motor Movement/Imagery Dataset | data or information resource, data set | Data set of over 1500 one- and two-minute EEG recordings, obtained from 109 volunteers. Subjects performed different motor/imagery tasks while 64-channel EEG were recorded using the BCI2000 system (http://www.bci2000.org). Each subject performed 14 experimental runs: two one-minute baseline runs (one with eyes open, one with eyes closed), and three two-minute runs of each of the four following tasks: # A target appears on either the left or the right side of the screen. The subject opens and closes the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the left or the right side of the screen. The subject imagines opening and closing the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject opens and closes either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject imagines opening and closing either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. The data are provided here in EDF+ format (containing 64 EEG signals, each sampled at 160 samples per second, and an annotation channel). | eeg, recording, motor, movement, imagery, eyes open, eyes closed, task, open fist, closed fist | has parent organization: PhysioNet | NIBIB EB006356; NIBIB EB00856 |
PMID:15188875 | Acknowledgement requested | nlx_84003 | SCR_004858 | EEG Motor Movement / Imagery Dataset | 2026-02-14 02:07:30 | 4 | |||||
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National Resource for Quantitative Functional MRI Resource Report Resource Website 1+ mentions |
National Resource for Quantitative Functional MRI (RRID:SCR_006716) | Resource for Quantitative Functional MRI | biomedical technology research center, training resource | Biomedical technology research center that provides expertise for the design of quantitative magnetic resonance imaging (MRI) and spectroscopy (MRS) data acquisition and processing technologies that facilitate the biomedical research of a large community of clinicians and neuroscientists in Maryland and throughout the USA. These methods allow noninvasive assessment of changes in brain anatomy as well as in tissue metabolite levels, physiology, and brain functioning while the brain is changing size during early development and during neurodegeneration, i.e. the changing brain throughout the life span. The Kirby Center has 3 Tesla and 7 Tesla state of the art scanners equipped with parallel imaging (8, 16, and 32-channel receive coils) and multi-transmit capabilities. CIS has an IBM supercomputer that is part of a national supercomputing infrastructure. Resources fall into the following categories: * MRI facilities, image acquisition, and processing * Computing facilities and image analysis * Novel statistical methods for functional brain imaging * Translating laboratory discoveries to patient treatment | quantitative magnetic resonance imaging, magnetic resonance spectroscopy, mri, fmri, function, metabolism, physiology, brain, neurodevelopment, neurodegeneration, image acquisition, image processing, computing, image analysis, statistical method, neuroimaging, development |
has parent organization: Kennedy Krieger Institute has parent organization: Johns Hopkins University; Maryland; USA |
NIBIB P41 EB015909; NCRR P41 RR015241 |
nlx_152634 | http://mri.kennedykrieger.org/nationalresource/index.html | SCR_006716 | Resource for Quantitative Functional Magnetic Resonance Imaging | 2026-02-14 02:07:31 | 1 | ||||||
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MNE software Resource Report Resource Website 50+ mentions |
MNE software (RRID:SCR_005972) | MNE | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics. | Magnetoencephalography data processing, electroencephaography data processing, data analysis, eeg, meg, linux, mac osx, human neurophysiological data, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MNE-BIDS is related to: MATLAB is related to: NumPy is related to: SciPy is related to: Matplotlib is related to: Mayavi: 3D Scientific Data Visualization and Plotting Software Project is related to: NiBabel |
NIBIB R01 EB009048; NIBIB P41 EB015896; NCRR P41 RR014075; NIDCD F32DC012456; NSF 0958669; NSF 1042134; European Research Council (ERC) StG-263584 |
PMID:24161808 PMID:24431986 |
Free, Available for download, Freely available | nlx_151346 | https://sources.debian.org/src/python3-mne/ http://www.nitrc.org/projects/mne http://www.nmr.mgh.harvard.edu/martinos/ncrr/sofMNE.html https://github.com/mne-tools/ https://mne.tools/ |
SCR_005972 | Minimum Norm Current Estimates Software, Minimum Norm Current Estimates, MNE tools for MEG and EEG data analysis, MNE-Python | 2026-02-15 09:19:06 | 97 | ||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | software application, data visualization software, data processing software, software resource, image analysis software | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-02-15 09:19:19 | 93 | |||||
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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 | portal, software resource, service resource, storage service resource, community building portal, data repository, data or information resource, software 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 - 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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 | 2026-02-15 09:18:31 | 338 | ||||
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IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | software application, image processing software, data processing software, software resource, source code, image analysis software | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-02-15 09:18:32 | 1585 | ||||
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Center for Integration of Medicine and Innovative Technology Resource Report Resource Website 1+ mentions |
Center for Integration of Medicine and Innovative Technology (RRID:SCR_003710) | CIMIT | organization portal, portal, funding resource, consortium, data or information resource | A non-profit consortium of Boston academic medical centers and universities (and growing) to accelerate the healthcare innovation cycle by fostering interdisciplinary, inter-institutional collaboration among experts in translational research, medicine, science, engineering, healthcare implementation and entrepreneurship in concert with industry, foundations and government to rapidly improve patient care. It concentrates on early stage, high-risk ideas, projects and supports them through to a commercial exit from academia. It provides innovators with resources to explore, develop and implement novel technological solutions for today's most urgent healthcare problems. CIMIT is dedicated to helping develop medical technology that will help both military and civilian patients. | device, procedure, diagnosis, healthcare, consortium, clinical, systems engineering, technology, patient care, translational research, medicine, science, engineering, innovation, consortium |
is listed by: Consortia-pedia has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Charles Stark Draper Laboratory |
United States Department of Defense ; Membership fees ; NIBIB |
nlx_157880 | SCR_003710 | Center for Integration of Medicine & Innovative Technology, Center for Integration of Medicine and Innovative Technology (CIMIT) | 2026-02-15 09:18:36 | 5 | |||||||
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Synapse Web Resource Report Resource Website 50+ mentions |
Synapse Web (RRID:SCR_003577) | training material, atlas, data or information resource, image collection, narrative resource | A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy. | electron microscopy, 3d reconstruction, neuroanatomy, astrocyte, axon, brain, cellular, dendrite, hippocampus, micrograph, microscopy, neurocytology, organelle, structure, synapse, tissue, ultrastructural, light microscopy, neuron, rat, experimental protocol, synapse structure |
is used by: NIF Data Federation has parent organization: University of Texas at Austin; Texas; USA |
The Human Brain Project ; NIDA R01 MH/DA 57351; NIMH R01 MH/DA 57351; NIBIB EB002170 |
Copyrighted, Acknowledgement required | nif-0000-00026 | SCR_003577 | SynapseWeb | 2026-02-15 09:18:32 | 69 | |||||||
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NITRC-IR Resource Report Resource Website 1+ mentions |
NITRC-IR (RRID:SCR_004162) | NITRC IR | catalog, database, image database, service resource, storage service resource, data repository, data or information resource, 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 | 2026-02-15 09:18:38 | 8 | ||||
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MRM NeAt (Neurological Atlas) Mouse Brain Database Resource Report Resource Website 1+ mentions |
MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) | MRM NeAt | database, atlas, reference atlas, image collection, data or information resource | Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data. | phenotype, mouse, brain, computational biology, in vivo, mouse brain atlas, magnetic resonance microscopy, mouse brain morphometry, image registration, in vitro, 3d brain atlas, adult mouse, male, c57bl/6j, autosegmentation, probabilistic atlas, t2 weighted protocol |
is related to: Mouse Brain Image Visualizer (MBIV) is related to: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery has parent organization: University of Florida; Florida; USA is parent organization of: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery |
National High Magnetic Field Laboratory ; NIBIB R01 EB 0023304; NCRR P41 RR16105; NIMH P50 MH58911 |
PMID:16165303 PMID:18958199 |
Registration required | nlx_59497 | http://brainatlas.mbi.ufl.edu | SCR_007053 | Magnetic Resonance Microimaging Neurological Atlas Mouse Brain Database, MRM Neurological Atlas Mouse Brain Database, C57BL/6J Mouse Atlas, Atlas of Adult C57BL/6J Mouse Brain, MRM NeAt Mouse Brain Database | 2026-02-15 09:19:27 | 8 | ||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | catalog, database, service resource, storage service resource, data repository, data or information resource | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | 2026-02-15 09:19:24 | 39 | ||||
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WFU PickAtlas Resource Report Resource Website 1000+ mentions |
WFU PickAtlas (RRID:SCR_007378) | PickAtlas | software application, image processing software, data processing software, software resource | A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | neuroanatomy, cytoarchitecture, fmri, matlab, brain, brain region, talairach daemon, analyze, atlas application, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Talairach Daemon has parent organization: Wake Forest School of Medicine; North Carolina; USA |
NIBIB 1R03EB008670 | PMID:12880848 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00358 | SCR_007378 | WFU_PickAtlas | 2026-02-15 09:19:34 | 1261 | |||||
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Charged Fluid Model for Brain Image Segmentation Resource Report Resource Website |
Charged Fluid Model for Brain Image Segmentation (RRID:SCR_008281) | CFMBIS | software application, data processing software, software resource, segmentation software, image analysis software | A computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data. Each interactive visualization element corresponding to the embedded function enables the end user to easily manipulate the image data. The visual environment of this tool provides an easy-to-use means of inspection and interpretation of image data using the LONI jViewbox library. CFMBIS uses the Java Image I/O plug-in architecture to read a wide variety of common medical image file formats. | plugin, software, 2D image, brain image segmentation, brain MR image, image analysis, segementation |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
Available for educational and research purposes only | nif-0000-23325 | SCR_008281 | 2026-02-15 09:19:46 | 0 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
