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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-08-04 09:42:24 | 160 | ||||||
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COST Resource Report Resource Website 1000+ mentions |
COST (RRID:SCR_014098) | COST | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:20 | 4519 | |||||||||
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BROCCOLI Resource Report Resource Website 10+ mentions |
BROCCOLI (RRID:SCR_014093) | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:20 | 21 | |||||||||
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3dsvm Resource Report Resource Website |
3dsvm (RRID:SCR_014083) | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:19 | 0 | |||||||||
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BrainCSI Resource Report Resource Website 1+ mentions |
BrainCSI (RRID:SCR_013244) | BrainCSI | data processing software, software application, software resource, image analysis software | A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images. | magnetic resonance spectroscopy, c++, console (text based), dicom, macos, microsoft, magnetic resonance, nifti, posix/unix-like, software, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
BSD License | nlx_155711 | http://www.nitrc.org/projects/braincsi | SCR_013244 | 2026-08-04 09:43:10 | 1 | |||||||
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NTU-DSI-122: a DSI template in ICBM-152 space Resource Report Resource Website 1+ mentions |
NTU-DSI-122: a DSI template in ICBM-152 space (RRID:SCR_014155) | radiographic image, map, data or information resource, image | A diffusion spectrum imaging (DSI) template constructed in the standard ICBM-152 space from 122 healthy adults. The template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets, rendering it to achieve a high anatomical matching to the ICBM-152 space. This template can serve as a representative DSI dataset for a healthy adult population. It is released in its original DWI format. | dsi, template, map, image, human brain | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:26095830 | Public, Available to the research community | SCR_014155 | 2026-08-04 09:43:21 | 1 | |||||||||
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FastICA Resource Report Resource Website 100+ mentions |
FastICA (RRID:SCR_013110) | FastICA | data processing software, software application, software resource, image analysis software | 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 | 2026-08-04 09:43:08 | 185 | |||||||
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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 | 2026-08-04 09:43:08 | 2 | |||||||
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Region to Region Resource Report Resource Website 1+ mentions |
Region to Region (RRID:SCR_016995) | data processing software, software application, software resource | Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another. | connectivity, pattern, region, neuroinformatics, region, receptive, field, model, visual, neuroscience, voxel, mapping, 3D, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Stony Brook University; New York; USA |
Free, Available for download, Freely available | SCR_016995 | 3-D Connective Field Modeling Toolbox | 2026-08-04 09:44:04 | 1 | |||||||||
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HeuDiConv: a heuristic-centric DICOM converter Resource Report Resource Website 10+ mentions |
HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) | HeuDiConv | data processing software, software application, software resource | Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts. | Flexible, DICOM, converter, organizing, brain, image, data, structured, directory, layout | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | http://www.nitrc.org/projects/heudiconv/ | SCR_017427 | heudiconv, heuristic-centric DICOM converter | 2026-08-04 09:44:13 | 28 | ||||||||
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NKI-RS Enhanced Sample Resource Report Resource Website 50+ mentions |
NKI-RS Enhanced Sample (RRID:SCR_010461) | Enhanced NKI-RS | data set, data or information resource | Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, lifespan, physiological assessment, psychological assessment, genetic |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: Mind Research Network - COINS is related to: NIMH Repository and Genomics Resources has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Public, Data Usage Agreement | nlx_157649 | SCR_010461 | Enhanced Nathan Kline Institute - Rockland Sample | 2026-08-04 09:42:46 | 97 | |||||
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minc-toolkit-testsuite Resource Report Resource Website |
minc-toolkit-testsuite (RRID:SCR_014139) | data set, data or information resource | Sample data in MINC format and collection of scripts to verify correct installation of minc-toolkit. | sample data set, minc, test, installation |
is used by: minc-toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
SCR_014139 | 2026-08-04 09:43:20 | 0 | |||||||||||
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High-quality diffusion-weighted imaging of Parkinsons disease Resource Report Resource Website |
High-quality diffusion-weighted imaging of Parkinsons disease (RRID:SCR_014121) | data set, data or information resource | A project which contains data and analysis pipelines for a set of 53 subjects in a cross-sectional Parkinsons disease (PD) study. The dataset contains diffusion-weighted images (DWI) of 27 PD patients and 26 age, sex, and education-matched control subjects. The DWIs were acquired with 120 unique gradient directions, b=1000 and b=2500 s/mm2, and isotropic 2.4 mm3 voxels. The acquisition used a twice-refocused spin echo sequence in order to avoid distortions induced by eddy currents. | data set, parkinson, diffusion weighted image | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | http://www.nitrc.org/ir//app/template/XDATScreen_report_xnat_projectData.vm/search_element/xnat:projectData/search_field/xnat:projectData.ID/search_value/parktdi | SCR_014121 | High quality DWI of Parkinsons Disease, High quality DWI of PD | 2026-08-04 09:43:20 | 0 | ||||||||
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Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) Resource Report Resource Website |
Efficient Longitudinal Upload of Depression in the Elderly (ELUDE) (RRID:SCR_014103) | ELUDE | data set, data or information resource | A longitudinal study of late-life depression at Duke University. There are 281 depressed subjects and 154 controls included. An MR scan of each subject was obtained every 2 years for up to 8 years (total of 1093 scans). Clinical assessments occurred more frequently and consists of a battery of psychiatric tests, including several depression-specific tests. | data set, longitudinal, depression, late life, mr |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Duke University; North Carolina; USA |
SCR_014103 | Efficient Longitudinal Upload of Depression in the Elderly | 2026-08-04 09:43:20 | 0 | |||||||||
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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 set, data or information resource | 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 | 2026-08-04 09:40:24 | 0 | |||||
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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, training resource, service 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 | 2026-08-04 09:40:22 | 1 | ||||||
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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 set, data or information resource | 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 | 2026-08-04 09:40:43 | 3 | |||||
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CANDI Share: Schizophrenia Bulletin 2008 Resource Report Resource Website 1+ mentions |
CANDI Share: Schizophrenia Bulletin 2008 (RRID:SCR_009451) | CANDI Share: Schizophrenia Bulletin 2008 | data set, data or information resource | This project hosts data for CANDI Share Schizophrenia Bulletin 2008 (reference below) as part of the CANDI Neuroimaging Access Point. This set includes preprocessed MRI images and segmentation results of all 4 diagnostic groups (Healthy Controls, N=29; Schizophrenia Spectrum, N=20; Bipolar Disorder with Psychosis, N=19; and Bipolar Disorder without Psychosis, N=35). Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46. | magnetic resonance, mri, segmentation, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: CANDI Neuroimaging Access Point |
Bipolar Disorder, Schizophrenia, Healthy, Bipolar Disorder without psychosis, Bipolar Disorder with psychosis, Psychosis | PMID:18003631 | Creative Commons Attribution License | nlx_155595 | SCR_009451 | 2026-08-04 09:42:23 | 2 | ||||||
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MRI Dataset for Hippocampus Segmentation Resource Report Resource Website |
MRI Dataset for Hippocampus Segmentation (RRID:SCR_009597) | Hippocampus Segmentation Dataset | data set, data or information resource | This dataset contains T1-weighted MR images of 50 subjects, 40 of whom are patients with temporal lobe epilepsy and 10 are nonepileptic subjects. Hippocampus labels are provided for 25 subjects for training. The users may submit their segmentation outcomes for the remaining 25 testing images to get a table of segmentation metrics. | hfh hippocampus segmentation, magnetic resonance, hippocampus, image collection, mri, segmentation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Epilepsy, Normal | PMID:21286946 | Other/Commercial license License | nlx_155797 | http://www.nitrc.org/projects/hippseg_2011 | SCR_009597 | 2026-08-04 09:42:26 | 0 | |||||
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Multi-Echo Independent Component Regression Group-Level Connectivity Dataset Resource Report Resource Website |
Multi-Echo Independent Component Regression Group-Level Connectivity Dataset (RRID:SCR_009508) | ME-ICR GroupInCorr Dataset | data set, data or information resource | Data set of an AFNI GroupInCorr session for multi-echo independent component regression (ME-ICR) for a cohort of 52 subjects. This dataset provides a high-quality atlas of seed-based functional connectivity with strong statistical conditioning. | computational neuroscience, independent component regression, afni, functional connectivity | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BIRN Data License, COINS Data Use Agreement | nlx_155668 | SCR_009508 | Multi-Echo Independent Component Regression (ME-ICR) Group-Level Connectivity (GroupInCorr) Dataset | 2026-08-04 09:42:23 | 0 |
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