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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Notion ResearchPACS Resource Report Resource Website |
Notion ResearchPACS (RRID:SCR_014154) | software application, software resource, standalone software | Standalone software designed to be used by radiology researchers for storage and anonymization of research images. | standalone software, radiology, storage, research image, anonymization, pacs | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community | SCR_014154 | 2026-09-19 12:58:11 | 0 | ||||||||||
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CUDA-SPHERE-FWD-MEEG Resource Report Resource Website |
CUDA-SPHERE-FWD-MEEG (RRID:SCR_013225) | CUDA-SPHERE-FWD-MEEG | software resource, software toolkit | A CUDA C based toolkit which provides a GPU based implementation of the spherical model forward solution for the 306 channel Elekta Neuromag MEG system and the EEG. The 1-Sphere forward solution for the MEG and the 4-Sphere forward solution for the EEG is implemented in CUDA C and an accelerated solution is obtained using the NVIDIA GPU when the solution is calculated for a large number of dipoles (on the order of 15000 and above) and sensor location. Speedup by a factor of 22 and 32 is obtained for the EEG and MEG solution respectively when compared to the fastest CPU implementation available in the public domain. The complete source code and pre-compiled binaries are also made available via an open source license (GPL Version 3). A CUDA enabled NVIDIA graphics card is required to use the software. | eeg, meg, electrocorticography, eeg modeling, forward - inverse, meg modeling, modeling | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License v3 | nlx_155725 | http://www.nitrc.org/projects/cuda_sphere_fwd | SCR_013225 | CUDA accelerated spherical model M/EEG, CUDA accelerated spherical model forward solution for EEG/MEG | 2026-09-19 12:58:09 | 0 | ||||||
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Neurodocker Resource Report Resource Website 1+ mentions |
Neurodocker (RRID:SCR_017426) | software application, software resource | Software tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12. | Generate, Dockerfile, singularity, recipe, neuroimaging, command-line, interface, minify, container | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | https://www.nitrc.org/projects/neurodocker/ | SCR_017426 | 2026-09-19 12:58:15 | 4 | |||||||||
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Hitachi Optical Topography System Resource Report Resource Website |
Hitachi Optical Topography System (RRID:SCR_000865) | Hitachi Optical Topography System | instrument supplier, material resource | An instrumental supplier which provides researchers and clinicians with sophisticated All-in-One solutions in the field of neuroscience. | hardware, nirs, fnir, optical imaging, optical imaging, physiological recording, scanner, fnirs neuroimaging, ultrasound, mri, x-ray, radiography, computed tomography | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155772 | http://www.nitrc.org/projects/hitachimedical | SCR_000865 | 2026-09-19 12:58:31 | 0 | |||||||
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ADHD-200 Preprocessed Data Resource Report Resource Website 1+ mentions |
ADHD-200 Preprocessed Data (RRID:SCR_000576) | ADHD-200 Preprocessed Data | data or information resource, data set | Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau | mri, fmri, brain, neuroimaging, attention deficit-hyperactivity disorder, anatomical, resting state, child, adolescent, human, young, early adult human, functional imaging, structural imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuro Bureau has parent organization: Neuro Bureau has parent organization: ADHD-200 Sample |
Attention deficit-hyperactivity disorder | Free, Public, Account required, Acknowledgement requested | nlx_144425 | http://www.nitrc.org/ir/app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:projectData.ID/search_value/adhd_200 | SCR_000576 | 2026-09-19 12:58:30 | 4 | ||||||
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Center for Functional Neuroimaging Technologies Resource Report Resource Website 1+ mentions |
Center for Functional Neuroimaging Technologies (RRID:SCR_001423) | CFNT | access service resource, biomedical technology research center, service resource, training resource | Biomedical technology research center that develops and applies innovative neuroimaging technologies and techniques to enable closer examination of the human brain, and thereby contribute to better understanding of the brain in health and disease. They develop new techniques and advance existing technologies for acquisition and analysis of functionally specific images of the working brain, with unprecedented physiological precision and spatiotemporal resolution. The research and development aims to improve and extend existing methods for non-invasive magnetic resonance image analysis and acquisition, electromagnetic source imaging, optical neuroimaging, and most recently, combined MR-PET neuroimaging. The Resource provides an essential interactive environment, within which an interdisciplinary team of highly skilled scientists, engineers, and clinicians with diverse expertise in multiple modalities and disciplines. The resource supports service use of the Center's facilities by neuroscientists throughout the country, provide extensive training opportunities for students, fellows, and staff scientists, and seek to advance the field of brain mapping through active dissemination of new knowledge and technology. | mri, neuroimaging, pet, acquisition, analysis, brain, electromagnetic source imaging, optical neuroimaging, multimodal, magnetic resonance, eeg, meg, electrocorticography, information resource, optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
NIBIB 5P41EB015896-18 | Free, Available for download, Freely available | nlx_152644 | http://www.nitrc.org/projects/cfnt | SCR_001423 | 2026-09-19 12:58:32 | 1 | ||||||
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Maps4Mipav (Exploratory JIST) Resource Report Resource Website |
Maps4Mipav (Exploratory JIST) (RRID:SCR_000613) | Maps4Mipav, | software resource, source code | The exploratory development tree of Java Image Science Toolkit (JIST), an extension to the MIPAV (Medical Image Processing, Analysis, and Visualization) plug-in framework that allows the user to design and execute pipelines, which are multi-stage processing tasks.. New features and designs are tested here before general release into the JIST project. JIST was formerly known as the MedIC Automated Pipeline Scheduler (MAPS). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit is related to: MIPAV: Medical Image Processing and Visualization |
Free, Available for download, Freely available | nlx_151345 | SCR_000613 | MedIC Automated Pipeline Scheduler Medical Image Processing Analysis and Visualization | 2026-09-19 12:58:30 | 0 | |||||||
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NIRx NIRS Neuroimaging Resource Report Resource Website 10+ mentions |
NIRx NIRS Neuroimaging (RRID:SCR_002491) | instrument supplier, material resource | Commercial technology solutions for NIRS neuroscience imaging applications. | hardware, image reconstruction, nirs, fnir, optical imaging, physiological recording, tomography, neuroimaging, adult, infant, child, imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: NIRStar is parent organization of: NIRSPORT |
Restricted | nlx_155886 | http://www.nitrc.org/projects/nirx | SCR_002491 | NIRx Optical Neuroimaging | 2026-09-19 12:58:34 | 21 | |||||||
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Beijing: Eyes Open Eyes Closed Study Resource Report Resource Website |
Beijing: Eyes Open Eyes Closed Study (RRID:SCR_001507) | Beijing EOEC | data or information resource, data set | Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed. | early adult human, resting state, fmri, diffusion tensor imaging, resting state fmri, eyes open, eyes closed, neuroimaging, mprage, image collection, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China (863) 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_152810 | SCR_001507 | Beijing Eyes Open Eyes Closed Study, Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Eyes Open Eyes Closed Sample, Eyes Open Eyes Closed Sample, BNU Eyes Open Eyes Closed Sample | 2026-09-19 12:58:33 | 0 | |||||
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Automated recognition of brain region mentions in neuroscience literature. Resource Report Resource Website 1+ mentions |
Automated recognition of brain region mentions in neuroscience literature. (RRID:SCR_002731) | WhiteText | data or information resource, data set | Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology. | brain region, annotation, journal of comparative neurology, neuroanatomy, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PubMed is related to: MEDLINE has parent organization: University of British Columbia; British Columbia; Canada |
PMID:19750194 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24027 | http://www.nitrc.org/projects/whitetext/ | SCR_002731 | WhiteText - annotated neuroscience text | 2026-09-19 12:58:35 | 3 | |||||
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HI-SPEED Software Packets Resource Report Resource Website 1+ mentions |
HI-SPEED Software Packets (RRID:SCR_009585) | HI-SPEED Software Packets | data processing software, software application, software resource | HI-SPEED Software Packets contain # unconstrained and constrained nonlinear least squares diffusion tensor estimation techniques, # 2-dimensional and 3-dimensional analytical (Shepp-Logan) magnetic resonance imaging phantoms in both the Fourier and image domains, # techniques for reporting the underlying signal-to-noise ratio in magnetic resonance (MR) images, # Probabilistic Identification and EStimation of NOise (PIESNO)---a technique for identifying noise-only pixels and estimating the underlying noise standard deviation in MR images, and # a signal-transformational technique for breaking the noise floor in MR images. Many more computational tools will be shared with users and developers as they become available. | reusable library, image reconstruction, java, modeling, magnetic resonance, os independent, statistical operation, tensor metric, mri, diffusion tensor mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
HI-SPEED Software Packets License | nlx_155771 | http://www.nitrc.org/projects/hispeed | SCR_009585 | 2026-09-19 12:55:59 | 1 | |||||||
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Age Related Atrophy Dataset Resource Report Resource Website |
Age Related Atrophy Dataset (RRID:SCR_009528) | Age Related Atrophy Dataset | data or information resource, data set, software resource, source code | Dataset of structural MR images of 70 subjects collected during 2008-2010 across a wide range of ages. The dataset also contains resting state fMRI for most subjects. The structural images are T1 weighted, T2 weighted-FLAIR, 25 direction DTI, and the T1 mapping DESPOT [1] sequence. Reconstructed T1 maps for each subject are also available. The aquisition protocol was designed to study structural differences between young and older adults including both shape and intensity changes. Anonymized DICOM image sessions and processed images for each subject are available. The data is licensed under the Creative Commons Attribution License. It may be used freely for commercial, academic, or other use, as long as the original source is properly cited. http://www.bsl.ece.vt.edu/index.php?page=ara-dataset | magnetic resonance, image collection, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
Aging | NIH Roadmap for Medical Research ; NCRR U54 RR021813 |
Creative Commons Attribution License | nlx_155692 | http://www.nitrc.org/projects/aradata | SCR_009528 | 2026-09-19 12:55:59 | 0 | |||||
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AMILab Resource Report Resource Website 1+ mentions |
AMILab (RRID:SCR_009525) | AMILab | data processing software, software application, software resource | An opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK. | active contour, analyze, animation, artifact removal, bshort/bfloat, c++, dicom, domain independent, filtering, format conversion, fourier transform, frequency domain, gnome, image display, intensity contour, kde, linux, macos, medial axis, microsoft, minc, motion analysis, nrrd, posix/unix-like, python, quality metrics, rendering, resampling, segmentation, shape analysis, software, spatial transformation, spline interpolation, surface rendering, temporal transformation, two dimensional display, visualization, volume rendering, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:22356993 | GNU Lesser General Public License | nlx_155687 | http://www.nitrc.org/projects/amilab | SCR_009525 | 2026-09-19 12:55:59 | 1 | ||||||
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fNIRS Data Analysis Environment Resource Report Resource Website 1+ mentions |
fNIRS Data Analysis Environment (RRID:SCR_009522) | fNIRS Data Analysis Environment | data processing software, image analysis software, software application, software resource | A data analysis environment for diffuse optical tomography (DOT) functional neuroimaging data. Developed to process data from steady-state time-series measurements, it allows for maximal flexibility in the number and positions of optodes. The central component is an application called NAVI. Features include: # An electronic ledger (records metadata for all data transformations). # Data conditioning (e.g., frequency-filtering, selection of data on the basis of signal-to-noise ratio.) # 2D or 3D image formation and display. # Interpretation: atlas-based mapping; automated anatomical labeling; GLM; data-driven methods (e.g., PCA, ICA); model-based (e.g., dynamic causal modeling) and data-driven (e.g., correlation) connectivity analysis. Another important component is the Brain Model Generator, which includes FEM meshes for all parts of the head accessible to DOT measurements. The user can input the numbers of optodes, and manually specify their locations or input tracking-system data. | optical imaging, diffuse optical tomography, functional neuroimaging, optical tomography | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155683 | SCR_009522 | 2026-09-19 12:55:59 | 1 | |||||||||
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CURRY Resource Report Resource Website 100+ mentions |
CURRY (RRID:SCR_009546) | CURRY | data processing software, software application, software resource | Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package. | multimodal, atlas, application, connectivity, analysis, computed, tomography, database, eeg, meg, electrocorticography, modeling, finite, element, format, conversion, forward, inverse, image, reconstruction, meg, mesh, generation, model, magnetic resonance, pet, spect, segmentation, simulation, spatial, transformation, volumetric, neuroimaging, FASEB list | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155726 | http://www.nitrc.org/projects/curry_7 | SCR_009546 | CURRY Scan 7 Neuroimaging Suite, CURRY 8, CURRY 7, CURRY Neuroimaging Suite | 2026-09-19 12:55:59 | 170 | ||||||
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FastICA Resource Report Resource Website 100+ mentions |
FastICA (RRID:SCR_013110) | FastICA | data processing software, image analysis software, software application, software resource | General-purpose unsupervised data-analysis tool, most often used for brain imaging data. | independent component analysis, magnetic resonance, statistical operatio, matlab |
is used by: ICASSO is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Aalto University; Espoo; Finland |
GNU General Public License | nlx_155758 | http://www.nitrc.org/projects/incf_fastica | SCR_013110 | 2026-09-19 12:56:01 | 200 | |||||||
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DTI Atlas Builder Resource Report Resource Website 1+ mentions |
DTI Atlas Builder (RRID:SCR_013112) | DTIAtlasBuilder | data processing software, software application, software resource | This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work, so be sure to have these installed on your computer: - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher If you download the package, be sure to have the glut library installed. | magnetic resonance, dti, atlas | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155738 | http://www.nitrc.org/projects/dtiatlasbuilder | SCR_013112 | 2026-09-19 12:56:01 | 2 | |||||||
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COST Resource Report Resource Website 1000+ mentions |
COST (RRID:SCR_014098) | COST | data processing software, image analysis software, software application, software resource | A tool that implements a graph-based connectivity assessment method. This method uses a multi-directional graph propagation method applied to sampled orientation distribution function (ODF), which can be computed directly from the original diffusion imaging data. | software tool, connectivity assessment, image analysis software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
SCR_014098 | Connectivity Orientation Spherical distribution Tool | 2026-09-19 12:56:02 | 4543 | |||||||||
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BROCCOLI Resource Report Resource Website 10+ mentions |
BROCCOLI (RRID:SCR_014093) | data processing software, image analysis software, software application, software resource | A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations. | software package, parallel analysis, fmri, non linear spatial normalization, brain | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | https://github.com/wanderine/BROCCOLI/ | SCR_014093 | 2026-09-19 12:56:02 | 22 | |||||||||
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3dsvm Resource Report Resource Website |
3dsvm (RRID:SCR_014083) | data processing software, image analysis software, software application, software resource | A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. | plugin, afni, svm light, support vector machine, image analysis software |
uses: Analysis of Functional NeuroImages is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Public | http://www.nitrc.org/projects/afni_3dsvm | SCR_014083 | 2026-09-19 12:56:02 | 0 |
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