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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Neuroscience Gateway
 
Resource Report
Resource Website
10+ mentions
Neuroscience Gateway (RRID:SCR_008915) NSG data or information resource, portal, project portal, software resource Web portal that allows free access to supercomputing resources for large scale modeling and data processing. Portal facilitates access and use of National Science Foundation (NSF) High Performance Computing (HPC) resources by neuroscientists. Large, scale, modeling, data, computing, neuroscience, neuron, BRAIN Initiative is recommended by: BRAIN Initiative
lists: ModelRun
is related to: XSEDE - Extreme Science and Engineering Discovery Environment
is related to: NEURON
is related to: GENESIS Neural Database and Modelers Workspace
has parent organization: San Diego Supercomputer Center
has parent organization: Neuroscience Information Framework
has parent organization: Yale School of Medicine; Connecticut; USA
BBSRC N005236;
NIBIB R01 EB023297;
NSF 1146949;
NSF 1339856;
NSF 1458495;
NSF 1458840
Free, Freely available nlx_151553, SCR_015767 http://www.nitrc.org/projects/nsg/ SCR_008915 Neuroscience Gateway - A Portal for Computational Neuroscience, Neuroscience Gateway, Neuroscience Gateway (NSG) Portal 2026-09-03 04:59:45 25
Brain Computer Interface 2000 Software Package
 
Resource Report
Resource Website
100+ mentions
Brain Computer Interface 2000 Software Package (RRID:SCR_007346) data processing software, software application, software resource BCI2000 is a general-purpose system for brain-computer interface (BCI) and adaptive neurotechnology research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. The mission of the BCI2000 project is to facilitate research and applications in the areas described. Their vision is that BCI2000 will become a widely used software tool for diverse areas of real-time biosignal processing. In order to achieve this vision, BCI2000 system is available for free for non-profit research and educational purposes. BCI2000 supports a variety of data acquisition systems, brain signals, and study/feedback paradigms. During operation, BCI2000 stores data in a common format (BCI2000 native or GDF), along with all relevant event markers and information about system configuration. BCI2000 also includes several tools for data import/conversion (e.g., a routine to load BCI2000 data files directly into Matlab) and export facilities into ASCII. BCI2000 also facilitates interactions with other software. For example, Matlab scripts can be executed in real-time from within BCI2000, or BCI2000 filters can be compiled to execute as stand-alone programs. Furthermore, a simple network-based interface allows for interactions with external programs written in any programming language. For example, a robotic arm application that is external to BCI2000 may be controlled in real time based on brain signals processed by BCI2000, or BCI2000 may use and store along with brain signals behavioral-based inputs such as eye-tracker coordinates. Because it is based on a framework whose services can support any BCI implementation, the use of BCI2000 provides maximum benefit to comprehensive research programs that operate multiple BCI2000 installations to collect data for a variety of studies. The most important benefits of the system in such situations are: - A Proven Solution - Facilitates Operation of Research Programs - Facilitates Deployment in Multiple Sites - Cross-Platform and Cross-Compiler Compatibility - Open Resource Sponsors: BCI2000 development is sponsored by NIH/NIBIB R01 and NIH/NINDS U24 grants. Keywords: General, Purpose, Systems, Brain, Computer, Interface, Research, Application, Brain, Diverse, Educational, Laboratory, Software, Network, Signals, Behavioral, Eye, Tracker, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: National Institutes of Health
NIBIB P41 EB018783;
NIBIB R01 EB026439;
NINDS U24 NS109103
nif-0000-00251 http://www.nitrc.org/projects/bci2000, http://www.bci2000.org, https://www.neurotechcenter.org/software SCR_007346 BCI2000 2026-09-03 05:00:14 180
LONI Java Image I/O Plugins
 
Resource Report
Resource Website
LONI Java Image I/O Plugins (RRID:SCR_008277) data processing software, software application, software resource Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.The plugins use Java Image I/O interfaces to read and write metadata and image data and can read and write AFNI, ANALYZE 7.5, DICOM, ECAT 7.2, GE 5.0, INTERFILE (including hrrt), MINC, NIFTI, and UCLA PACS file formats. All source code is provided and usage examples are included. plugin, MRI, software, visualization, data processing 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
Available for educational and research purposes only nif-0000-23320 SCR_008277 2026-09-03 05:00:45 0
Homer2
 
Resource Report
Resource Website
100+ mentions
Homer2 (RRID:SCR_009586) data processing software, image analysis software, software application, software resource Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative is recommended by: BRAIN Initiative
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: NIRx2nirs: A NIRx to .nirs data converter
NCRR P41 RR14075;
NIBIB EB025145;
NIBIB R01 EB006385
Free, Available for download, Freely available nlx_155773 http://www.nitrc.org/projects/homer2, https://homer-fnirs.org/ SCR_009586 HOMER1, Photon Migration Imaging toolbox 2026-09-03 05:00:03 250
Center for Imaging of Neurodegenerative Diseases
 
Resource Report
Resource Website
Center for Imaging of Neurodegenerative Diseases (RRID:SCR_001968) CIND data or information resource, organization portal, portal Biomedical technology research center that develops and validates new imaging methods for detecting brain abnormalities in neurodegenerative diseases, including Alzheimer's disease, vascular dementia, frontotemporal dementia, Parkinson's disease, as well as epilepsy, depression, and other conditions associated with nerve loss in the brain. As people around the globe live longer, the impact of neurodegenerative diseases is expected to increase further with dire social and economical consequences for societies if no effective treatments are developed soon. The development at CIND is aimed to improve magnetic resonance imaging (MRI). The ultimate goal of the scientific program is to identify imaging markers that improve accuracy in diagnosing neurodegenerative diseases at early stages, achieve more reliable prognoses of disease progression, and facilitate the discovery of effective treatment interventions. In addition to addressing the general needs for studying neurodegenerative diseases, another focus of CIND concerns brain diseases associated with military service and war combat, such as post traumatic stress disorder (PTSD), brain trauma, gulf war illness and the long-term effects of these conditions on the mental health of veterans. The symbiosis between CIND and the Veterans Administration Medical Center in San Francisco makes this program uniquely suited to serve military veterans. Biomedical Technology Research Center, depression, mri, imaging, neuroimaging has parent organization: University of California at San Francisco; California; USA Neurodegenerative disease, Alzheimer's disease, Vascular dementia, Frontotemporal dementia, Parkinson's disease, Epilepsy, Depressive Disorder, Post-Traumatic Stress Disorder, Brain injury, Gulf war illness NIBIB THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10539 http://www.cind.research.va.gov/index.asp SCR_001968 UCSF Center for Imaging of Neurodegenerative Diseases 2026-09-03 04:59:48 0
DRIFTER
 
Resource Report
Resource Website
10+ mentions
DRIFTER (RRID:SCR_014937) data processing software, image analysis software, software application, software resource Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data. bayesian, physiological noise, fMRI, algorithm, cardiac, respiratory, image anaylsis, bold signal has parent organization: Aalto University; Espoo; Finland NICHD R01HD040712;
NINDS R01NS037462;
NINDS R01NS048279;
NCR P41RR014075;
NIMH R01MH083744;
NIDCD R21DC010060;
NIBIB R21EB007298;
National Science Council Taiwan NSC 98-2320-B-002-004-MY3;
National Science Council Taiwan NSC 100-2325-B-002-046;
National Health Research Institute Taiwan NHRI-EX100-9715EC;
Academy of Finland 124698;
Academy of Finland 125349;
Academy of Finland 127624;
Academy of Finland 129670;
Academy of Finland 218054;
Academy of Finland 218248
PMID:22281675 Free, Available for download, Acknowledgement requested SCR_014937 DRIFTER Toolbox 2026-09-03 05:00:55 28
TRACULA
 
Resource Report
Resource Website
10+ mentions
TRACULA (RRID:SCR_013152) TRACULA data processing software, software application, software resource Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging is related to: FreeSurfer
has parent organization: Harvard Medical School; Massachusetts; USA
Aging NIH Blueprint for Neuroscience Research ;
Ellison Medical Foundation ;
NIBIB EB008129;
NIMH U01-MH093765;
NCRR P41-RR14075;
NCRR U24-RR021382;
NIBIB R01-EB006758;
NIA R01-AG022381;
National Center for Complementary and Alternative Medicine RC1-AT005728;
NINDS R01-NS052585;
NINDS R21-NS072652;
NINDS R01-NS070963
PMID:22016733 nlx_143919 SCR_013152 TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy 2026-09-03 05:00:52 17
CAWorks
 
Resource Report
Resource Website
1+ mentions
CAWorks (RRID:SCR_014185) data processing software, image analysis software, software application, software resource A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit. image analysis software, computational anatomy, shape analysis, plugin, subcortex, landmark placement is used by: Northwestern University Schizophrenia Data and Software Tool (NUSDAST)
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Johns Hopkins University; Maryland; USA
NIMH 1R01 MH084803;
NIBIB R01 EB008171;
NIA 5U01AG033655;
NCRR P41 RR015241;
NIBIB R01 EB000975
Available to the research community http://www.cis.jhu.edu/software/caworks/ SCR_014185 Computational Anatomy Works 2026-09-03 05:00:08 2
Neural Ideal
 
Resource Report
Resource Website
Neural Ideal (RRID:SCR_017448) data processing software, software application, software resource Software package for extracting neural activity codes. Extracting, neural, activity, code, BRAIN Initiative is recommended by: BRAIN Initiative
is related to: MATLAB
NIBIB EB022862 Free, Available for download, Freely available SCR_017448 2026-09-03 05:00:31 0
Neuron Tools
 
Resource Report
Resource Website
1+ mentions
Neuron Tools (RRID:SCR_017450) data processing software, software application, software resource Software tools for converting data files into persistence diagrams and distance matrices. Converting, data, file, diagram, distance, matice, BRAIN Initiative is recommended by: BRAIN Initiative NIBIB EB022899 Free, Available for download, Freely available SCR_017450 2026-09-03 05:01:01 3
Open Anatomy Project
 
Resource Report
Resource Website
Open Anatomy Project (RRID:SCR_022141) data or information resource, portal, project portal Project aims to change anatomy atlas by building atlases through open data, community based collaborative development, and free distribution of medical knowledge. Provides access to several 2D and 3D browser based tools. Atlas, Brigham and Women's Hospital in Boston, digital anatomy atlas, open data, community based collaborative development, medical knowledge NCRR ;
NIBIB
Free, Freely available SCR_022141 The Open Anatomy Project 2026-09-03 05:00:10 0
μManager
 
Resource Report
Resource Website
100+ mentions
μManager (RRID:SCR_016865) microManager software resource Software package for control of automated microscopes. Cross-platform desktop application, to control a motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. control, automated, microscope, imaging, Open Imaging is listed by: Debian
has parent organization: University of California at San Francisco; California; USA
is a plug in for: ImageJ
Sandler Foundation ;
NIBIB R01 EB007187
Free, Available for download, Freely available https://micro-manager.org/wiki/Download_Micro-Manager_Latest_Release, https://sources.debian.org/src/micromanager/ SCR_016865 Micro-Manager, micro-Manager 2026-09-03 04:54:04 152
Mediation Analysis of Causality under Confounding
 
Resource Report
Resource Website
Mediation Analysis of Causality under Confounding (RRID:SCR_017442) MACC data analysis software, data processing software, software application, software resource Software package to perform causal mediation analysis under confounding or correlated errors. Includes single level mediation model, two level and three level mediation model for data with hierarchical structures. Under two or three level mediation model, correlation parameter is identifiable and is estimated based on hierarchical likelihood, marginal likelihood or two stage method. Casual, mediation, analysis, confounding, correlated, error, data, hierarchical, structure, parameter, BRAIN Initiative is recommended by: BRAIN Initiative
is listed by: CRAN
NIBIB EB022911 Free, Available for downloads, Freely available SCR_017442 Mediation Analysis of Causality under Confounding, macc 2026-09-03 04:54:28 0
NEURON
 
Resource Report
Resource Website
100+ mentions
NEURON (RRID:SCR_017449) simulation software, software application, software resource Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software. Computational, neurophysiology, model, neuron, network, building, BRAIN Initiative is recommended by: BRAIN Initiative
has parent organization: Yale University; Connecticut; USA
NIBIB EB022903 Free, Available for download, Freely available https://github.com/neuronsimulator/nrn SCR_017449 2026-09-03 04:54:24 244
PhysioNet
 
Resource Report
Resource Website
500+ mentions
PhysioNet (RRID:SCR_007345) PhysioNet analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material. physiologic, physiology, signal, software, research, biomedical, cardiopulmonary, neural, healthy, patient, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, cardioogy, computation, physiologic signal, workspace, time series, FASEB list, DRKB 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: DataCite
is listed by: re3data.org
is listed by: FAIRsharing
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
is parent organization of: CHB-MIT Scalp EEG Database
is parent organization of: EEG Motor Movement/Imagery Dataset
is parent organization of: Sleep-EDF Database
Aging NIBIB ;
NIGMS ;
NIH EB037545
PMID:22256277
PMID:14716615
PMID:14632011
PMID:11446213
PMID:10851218
Free, Freely available r3d100011561, DOI:10.17616/R3D06S, nif-0000-00250, DOI:10.25504/FAIRsharing.bemzxg, DOI:10.13026 https://doi.org/10.17616/R3D06S, https://doi.org/10.17616/r3d06s, https://doi.org/10.13026/, https://dx.doi.org/10.13026/, https://fairsharing.org/10.25504/FAIRsharing.bemzxg, https://doi.org/10.17616/R3D06S SCR_007345 Physionet: The Research Resource for Complex Physiologic Signals, PhysioNet, PhysioNet: The Research Resource for Complex Physiologic Signals 2026-09-03 04:58:07 841
Lightweight Data Pipeline
 
Resource Report
Resource Website
Lightweight Data Pipeline (RRID:SCR_014135) data processing software, software application, software resource, workflow software A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing. workflow software, framework, processing pipeline, configurable shell script, cluster processing is used by: NCANDA: Data Integration Component
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
NIAAA U01 AA021697;
NIBIB R01 EB008381
Available to the research community SCR_014135 2026-09-03 04:52:28 0
SCORE
 
Resource Report
Resource Website
100+ mentions
SCORE (RRID:SCR_014165) data or information resource, experimental protocol, narrative resource A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. experiment protocol, method, different image algorithm, quantitative score is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Utah; Utah; USA
NLM HHSN276201000584P;
NIBIB 1R41 EB011796
SCR_014165 2026-09-03 04:52:29 481
National Biomedical Electron Paramagnetic Resonance Center
 
Resource Report
Resource Website
National Biomedical Electron Paramagnetic Resonance Center (RRID:SCR_006601) National Biomedical EPR Center, EPR Center biomedical technology research center, training resource Biomedical technology research center focusing on technological innovation and application of new techniques to biological problems. The main areas of research are free radicals, spin labeling, metal complexes, and metallo proteins. Spectrometers are available for S-, X-, L-, Q- , and W-band EPR, many with ENDOR, ELDOR, saturation-transfer, saturation-recovery, and multiquantum capabilities. * Development of multiquantum Q- and W-band spectrometers, including multiquantum ELDOR, development of time-locked sub-sampling (TLSS) for broadband detection of periodically modulated signals * Development of loop-gap resonators using finite element modeling of Maxwell''s equations * Application of multifrequency (1 to 100 GHz) electron paramagnetic resonance (EPR) to characterize paramagnetic centers * Study of relaxation processes using multifrequency pulse saturation recovery * Use of nitroxide radical spin labels to measure translational and rotational diffusion in biological systems, site-directed spin labeling (SDSL), and use of EPR for the detection of nitric oxide and oxy radicals spectrometer, electron paramagnetic resonance, free radical, spin labeling, metal complex, metallo protein has parent organization: Medical College of Wisconsin; Wisconsin; USA NIBIB nlx_152655 SCR_006601 National Biomedical EPR 2026-09-03 05:06:29 0
MIALAB - Resting State Data
 
Resource Report
Resource Website
10+ mentions
MIALAB - Resting State Data (RRID:SCR_008914) data or information resource, data set An MRI data set that demonstrates the utility of a mega-analytic approach by identifying the effects of age and gender on the resting-state networks (RSNs) of 603 healthy adolescents and adults (mean age: 23.4 years, range: 12-71 years). Data were collected on the same scanner, preprocessed using an automated analysis pipeline based in SPM, and studied using group independent component analysis. RSNs were identified and evaluated in terms of three primary outcome measures: time course spectral power, spatial map intensity, and functional network connectivity. Results revealed robust effects of age on all three outcome measures, largely indicating decreases in network coherence and connectivity with increasing age. Gender effects were of smaller magnitude but suggested stronger intra-network connectivity in females and more inter-network connectivity in males, particularly with regard to sensorimotor networks. These findings, along with the analysis approach and statistical framework described, provide a useful baseline for future investigations of brain networks in health and disease. fmri, functional connectivity, resting-state, independent component analysis, connectome, adolescent, adult, mri, resting state network, connectivity, dataset has parent organization: MIALAB - Medical Image Analysis Lab Aging NRC Bilatgrunn ;
NIBIB 1R01-EB006841;
NIBIB 1R01- EB005846;
NIBIB 2R01-EB000840;
NIBIB 1 P20 RR021938-01;
DOE DE-FG02-08ER64581;
NIMH 1R01-MH072681-01;
John Templeton Foundation grant 12456;
NIAAA 1P20 AA017068;
NINDSR21NS064464 ;
NIDA1 R03 DA022435-01A1 ;
NIDA1 R03 DA024212-01A1 ;
NIDA KO1-DA021632-02
PMID:21442040 nlx_151552 SCR_008914 Medical Image Analysis Laboratory - Resting State Data, MIA Laboratory - Resting State Data, Medical Image Analysis Lab - Resting State Data, Medical Image Analysis (MIA) Laboratory - Resting State Data 2026-09-03 05:06:24 10
Neuroimage Analysis Center
 
Resource Report
Resource Website
1+ mentions
Neuroimage Analysis Center (RRID:SCR_008998) NAC biomedical technology research center, training resource Biomedical Technology Resource Center that develops image processing and analysis techniques for basic and clinical neurosciences. The NAC research approach emphasizes both specific core technologies and collaborative application projects. The core activity of the center is the development of algorithms and techniques for postprocessing of imaging data. New segmentation techniques aid identification of brain structures and disease. Registration methods are used for relating image data to specific patient anatomy or one set of images to another. Visualization tools allow the display of complex anatomical and quantitative information. High-performance computing hardware and associated software techniques further accelerate algorithms and methods. Digital anatomy atlases are developed for the support of both interactive and algorithmic computational tools. Although the emphasis of the NAC is on the dissemination of concepts and techniques, specific elements of the core software technologies have been made available to outside researchers or the community at large. The NAC's core technologies serve the following major collaborative projects: Alzheimer's disease and the aging brain, morphometric measures in schizophrenia and schizotypal disorder, quantitative analysis of multiple sclerosis, and interactive image-based planning and guidance in neurosurgery. One or more NAC researchers have been designated as responsible for each of the core technologies and the collaborative projects. brain, neuroimaging, image processing, image analysis, postprocessing, segmentation, registration, algorithm, technique, brain structure, visualization, neurosurgery has parent organization: Harvard Medical School; Massachusetts; USA Alzheimer's disease, Aging, Schizophrenia, Schizotypal disorder, Multiple Sclerosis, Neurosurgery NIBIB P41 EB015902;
NCRR P41 RR13218
nlx_152643 SCR_008998 Neuroimaging Analysis Center 2026-09-03 05:06:26 8

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