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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas Resource Report Resource Website |
McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas (RRID:SCR_008793) | MNI Cynomolgus Macaque Atlas | reference atlas, atlas, data or information resource | A reference atlas of cynomolgus macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual cynomolgus monkeys and studies. We have used MRI volumes from a group of 18 normal adult cynomulgus monkeys (Macaca fascicularis) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous cynomolgus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the cynomolgus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format. | long-tailed macaque, brain, early adult, mri, neuroanatomy | has parent organization: McConnell Brain Imaging Center | Normal | PMID:21256229 | nlx_144294 | SCR_008793 | BIC MNI Cynomolgus Macaque Atlas | 2026-08-04 09:42:13 | 0 | ||||||
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NIHPD Objective 2 atlases (birth - 4.5 years) Resource Report Resource Website 1+ mentions |
NIHPD Objective 2 atlases (birth - 4.5 years) (RRID:SCR_008795) | NIHPD Objective 2 atlases (birth - 4.5 years) | reference atlas, atlas, data or information resource | An unbiased magnetic resonance imaging template brain volume for pediatric data from birth to 4.5y age range. These volumes were created using 317 scans from 108 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Templates are constructed for different age ranges. Each age range includes an average T1w, T2w, PDw maps normalized between 0 and 100. Also each age range includes a binary brain mask. Tools for using these atlases can be found in the Software section. | pediatric, child, mri, young human, brain, template | has parent organization: McConnell Brain Imaging Center | Aging | nlx_144296 | SCR_008795 | McConnell Brain Imaging Center NIHPD Objective 2 atlases (birth - 4.5 years), BIC NIHPD Objective 2 atlases (birth - 4.5 years) | 2026-08-04 09:42:14 | 4 | |||||||
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McConnell Brain Imaging Center MNI Rhesus Macaque Atlas Resource Report Resource Website 1+ mentions |
McConnell Brain Imaging Center MNI Rhesus Macaque Atlas (RRID:SCR_008790) | MNI Rhesus Macaque Atlas | reference atlas, atlas, data or information resource | A reference atlas of rhesus macaque monkey magnetic resonance images that offers a common stereotaxic reference frame. The atlas can be used to localize anatomical and functional information in an organized and reliable way for comparison across individual rhesus monkeys and studies. We have used MRI volumes from a group of 7 normal adult rhesus monkeys (Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous rhesus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the rhesus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format. | rhesus monkey, brain, early adult | has parent organization: McConnell Brain Imaging Center | PMID:21256229 | nlx_144293 | SCR_008790 | BIC MNI Rhesus Macaque Atlas | 2026-08-04 09:42:14 | 1 | |||||||
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Brain.io Resource Report Resource Website |
Brain.io (RRID:SCR_014527) | portal, project portal, data or information resource | A startup research, development and innovation company based in The Grand Duchy of Luxembourg working on four major areas: Open Research, as Information Hub; Information Technology, as The Common Brain; Collective Awareness, as Manifesto; and Biophysics, as Human Extensibility. The Information Hub researches a methodology to conduct open research using a collaborative approach designed for multi-disciplinary interventions, multi-scope goal alignment, advanced analytics and a unified research experience for international cooperation. The Common Brain researches an open source intelligent architecture for future internet, one that is deeply sustainable over a highly distributed hybrid network, self-governed, heterogenous, and logical. Manifesto researches a methodology for a collaborative approach for policy making, open standardization, accreditation, verification and compliance. Human Extensibility researches the establishment of the scientific ground for a field of science concerned with the study of the physics and physiology of the human being, to provide techniques and genetic algorithms for human extensibility. | brain, startup, research, information hub, common brain, manifesto, human extensibility, open research, information technology, collective awareness, biophysics | SCR_014527 | Brain.io The Path to Paradigm Shift | 2026-08-04 09:43:27 | 0 | |||||||||||
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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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brainlife.io Resource Report Resource Website 1+ mentions |
brainlife.io (RRID:SCR_016513) | portal, data or information resource | Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain. | human, brain, life, data, application, technology, share, open, software, reproducible, code, dataset, |
has parent organization: Indiana University Bloomington; Indiana; USA works with: brainlife |
NSF BCS 1734853; NSF IIS 1636893 |
DOI:10.1038/s41597-019-0073-y | Public, Free, Freely available, Login required | https://github.com/brain-life | SCR_016513 | 2026-08-04 09:43:55 | 1 | |||||||
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BraTS Resource Report Resource Website 1+ mentions |
BraTS (RRID:SCR_016214) | portal, organization portal, data or information resource | Organization that provides a conference about the methods for the segmentation of brain tumors in magnetic resonance imaging (MRI) scans. Its conferences utilize multi-institutional pre-operative MRI scans and focus on the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. | brain, neuroscience, tumor, cancer, segmentation, mri, neuroimaging, glioma, patient, conference, event | SCR_016214 | BraTS: Multimodal Brain Tumor Segmentation, Multimodal Brain Tumor Segmentation | 2026-08-04 09:43:51 | 7 | |||||||||||
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BIDS Validator Resource Report Resource Website 10+ mentions |
BIDS Validator (RRID:SCR_017255) | data processing software, software application, software resource | Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure. | BIDS, NeuroImaging, Neuroscience, check, folder, structure, compliance, data, standard, brain, imaging | is listed by: OMICtools | Laura and John Arnold Foundation ; NIBIB R01 EB020740 |
PMID:28278228 | Free, Available for download, Freely available | http://bids-standard.github.io/bids-validator/ | SCR_017255 | Brain Imaging Data Structure (BIDS) Validator | 2026-08-04 09:44:07 | 20 | ||||||
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Compilation of Genetics Resource Databases Resource Report Resource Website 10+ mentions |
Compilation of Genetics Resource Databases (RRID:SCR_017501) | portal, data or information resource | Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse. | Genetic, data, brain, atlas, information, National, Institute, Drug, Abuse, FASEB list | Restricted | SCR_017501 | 2026-08-04 09:44:10 | 49 | |||||||||||
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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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Mouse Connectome Project Resource Report Resource Website |
Mouse Connectome Project (RRID:SCR_017313) | MCP | portal, project portal, data or information resource | Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks. | mesoscale, connectivity, atlas, C57Black/6, mouse, brain, neural, network |
is used by: BICCN has parent organization: University of Southern California; Los Angeles; USA |
NIH | Free, Freely available | SCR_017313 | The Mouse Connectome Project, Mouse Connectome Project | 2026-08-04 09:44:08 | 0 | |||||||
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Mononucleotide Repeat Frameshift Portal Resource Report Resource Website |
Mononucleotide Repeat Frameshift Portal (RRID:SCR_021125) | MORF | portal, organization portal, data or information resource | Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide. | Sparsely label genetically defined neuronal populations, reporter mouse lines, Cre-dependent sparse cell labeling methodology, MORF stochastic translational switch, integrating molecular, morphological properties, connectomic properties, unbiased classification, neuronal cell types, brain | has parent organization: University of California at Los Angeles; California; USA | PMID:32795398 | Free, Freely available | SCR_021125 | MOnonucleotide Repeat Frameshift, MORF portal | 2026-08-04 09:44:43 | 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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Arredondo ANT fNIRS dataset1 Resource Report Resource Website |
Arredondo ANT fNIRS dataset1 (RRID:SCR_002653) | AAF Data, AAF Data1, AF Data, AF Data1 | data set, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 12, 2017. Dataset in Bilingual exposure optimizes left-hemisphere dominance for selective attention processes in the developing brain by Arredondo, Su, Satterfield, & Kovelman (XX) Does early bilingual exposure alter the representations of cognitive processes in the developing brain? Theories of bilingual development have suggested that bilingual language switching might improve children''s executive function and foster the maturation of prefrontal brain regions that support higher cognition. To test this hypothesis, we used functional Near Infrared Spectroscopy to measure brain activity in Spanish-English bilingual and English-monolingual children during a visuo-spatial executive function task of attentional control (N=27, ages 7-13). Prior findings suggest that while young children start with bilateral activation for the task, it becomes right-lateralized with age (Konrad et al., 2005). Indeed monolinguals showed bilateral frontal activation, however young bilinguals showed greater activation in left language areas relative to right hemisphere and relative to monolinguals. The findings suggest that bilingual experience optimizes attention mechanisms in the language hemisphere, and highlight the importance of early experiences for neurodevelopmental plasticity of higher cognition. These data are made available from Ioulia Kovelman''s Language and Literacy Lab at University of Michigan and may be exported through the NIF Data Federation. To cite these data please use this text Data were published by Arredondo et al. (XX) and made available via the NIF at XX |
attention, functional near infrared spectroscopy, fnirs, bilingualism, language, child, ant, developing, brain |
is used by: NIF Data Federation has parent organization: University of Michigan; Ann Arbor; USA |
Healthy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156086 | SCR_002653 | ANT fNIRS Dataset1, ANT fNIRS Data Set1, Arredondo ANT fNIRS Data Set 1, Arredondo ANT fNIRS Data Set1, ANT fNIRS Data Set 1 | 2026-08-04 09:40:42 | 0 | ||||||
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GSE4271 Resource Report Resource Website 50+ mentions |
GSE4271 (RRID:SCR_003643) | GSE4271 | data set, data or information resource | Curated data set from a study that investigated 77 primary high-grade astrocytomas and 23 matched recurrences so that changes in gene expression related to both survival and disease progression can be identified. Samples in the study include WHO grade III and IV astrocytomas with a wide range of survival times. | adult human, brain, gene expression |
is related to: Gene Expression Omnibus has parent organization: RanchoBiosciences |
Cancer, Astrocytoma | Free, Public | nlx_157794 | SCR_003643 | 2026-08-04 09:40:57 | 60 | |||||||
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Neurophysiology Imaging Facility Resource Report Resource Website |
Neurophysiology Imaging Facility (RRID:SCR_004080) | NIF | access service resource, core facility, service resource | Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates. | mri, fmri, neuroimaging, neurophysiology, brain | has parent organization: National Institute of Mental Health | NIMH ; NINDS ; NEI |
nlx_158530 | SCR_004080 | Neurophysiology Imaging Facility (NIF) | 2026-08-04 09:41:03 | 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 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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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 | 2026-08-04 09:41:41 | 1 | ||||||
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Integrated Nervous System Connectivity Resource Report Resource Website |
Integrated Nervous System Connectivity (RRID:SCR_006391) | NSC | data set, data or information resource | A data set of connectivity statements from BAMS, CoCoMac, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal Table of Temporal-Lobe.com, and Avian Brain Circuitry Database. The data set lists which brain sites connectivity is to and from, the organism connectivity is mapped in, and journal references. | connectivity, nervous system, macaque, brain, bird, data set |
uses: Avian Brain Circuitry Database uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Connectome Wiki uses: BrainMaps.org uses: CoCoMac uses: Brain Architecture Management System uses: BlueBrain Bluima Connectivity is used by: NIF Data Federation has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the terms of use by the original resource | nif-0000-07732 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8 https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-8, http://neuinfo.org/nif/nifgwt.html?query=nif-0000-07732, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-07732-1 | SCR_006391 | NIF Integrated Nervous System Connectivity View, Neuroscience Information Framework Integrated Nervous System Connectivity, Integrated NSC View, Integrated NSC, NIF NSC, NIF Integrated NSC, Integrated Nervous System Connectivity View, Nervous System Connectivity | 2026-08-04 09:41:35 | 0 |
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