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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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National Chimpanzee Brain Resource Resource Report Resource Website 10+ mentions |
National Chimpanzee Brain Resource (RRID:SCR_019183) | NCBR | storage service resource, data or information resource, atlas, service resource, portal, data repository | Collection and distribution of chimpanzee neuroimaging data and postmortem brain tissue. Portal to access chimpanzee brain atlas tools, data repository, bibliography of publications, educational information, and links to other chimpanzee brain resources and datasets on the Internet. Serves as repository for in vivo structural MRI scans of chimpanzee brains, in vivo and postmortem diffusion tensor images (DTI), as well as postmortem fixed and frozen brain specimens. | Chimpanzee, Pan Troglodytes, Brain, MRI, DTI, chimpanzee neuroimaging data, postmortem brain tissue, chimpanzee brain atlas |
is related to: George Washington University; Washington D.C.; USA is related to: University of Texas MD Anderson Cancer Center is related to: Yerkes National Primate Research Center |
National Institute of Neurological Disorders and Stroke | Free, Freely available | SCR_019183 | 2026-02-17 10:03:53 | 31 | ||||||||
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Brain Imaging Analysis Kit Resource Report Resource Website 10+ mentions |
Brain Imaging Analysis Kit (RRID:SCR_014824) | BrainIAK | software application, data processing software, software resource, software toolkit, image analysis software | Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data. | brain, python, module, imaging, fmri, data, analysis, neuroimaging |
is related to: Intel has parent organization: Princeton University; New Jersey; USA |
Free, Available for download, Freely available | https://github.com/brainiak/brainiak | SCR_014824 | BrainIAK, Brain Imaging Analysis Kit, Brain Imaging Analysis Kit (BrainIAK) | 2026-02-17 10:02:42 | 26 | |||||||
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Braineac Resource Report Resource Website 10+ mentions |
Braineac (RRID:SCR_015888) | data or information resource, database, web application, software resource | Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | has parent organization: UK Brain Expression Consortium | Normal | PMID:25174004 | Public, Free, Available for download | SCR_015888 | 2026-02-17 10:02:55 | 49 | ||||||||
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CLIMB Lesion Symptom Mapping Software Resource Report Resource Website 1+ mentions |
CLIMB Lesion Symptom Mapping Software (RRID:SCR_018298) | CLSM | data analysis software, software application, data processing software, software resource | Software package that performs several multivariate and mass univariate lesion symptom mapping analyses. Uses patient imaging lesion masks of brain insults and correlates them in multiple ways with patient behavioral and covariate data. Several permutation based SPMs are computed along with power, variance explained, and lesion coverage maps. | Multivariate analysis, principal component analysis, brain, patient behavioral data, covariate data | NIDCD R01 DC016345; VA Clinical Science Grant |
Free, Available for download, Freely available | SCR_018298 | CLIMB Lesion Symptom Mapping | 2026-02-17 10:03:46 | 2 | ||||||||
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QModeling Resource Report Resource Website 1+ mentions |
QModeling (RRID:SCR_016358) | software application, data processing software, data analysis software, software resource, software toolkit, image analysis software | Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences. | statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequence |
is related to: University of Malaga; Andalusia; Spain is related to: MATLAB |
DOI:10.1007/s12021-018-9384-y | Free, Available for download, Available after registration | SCR_016358 | 2026-02-17 10:03:24 | 1 | |||||||||
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Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | data analysis software, software application, data processing software, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | , Brain, Gene, Expression, Analysis, toolbox | 2026-02-17 10:02:52 | 1 | |||||||||
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AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders Resource Report Resource Website |
AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders (RRID:SCR_005336) | AGNOSIA APHASIA APRAXIA and Related Terms for Cognitive Behavioral and Neurological Disorders | data or information resource, data set, terminological resource | Compilation terms with definitions that describe altered states that are associated with brain injury (e.g., trauma, stroke, tumor) or with developmental deficits. Although the list deals with primarily CNS-associated disorders, in some cases the term does not distinguish between a CNS cause or a peripheral or neuromuscular cause. Terms that are primarily psychiatric diagnoses (e.g., schizophrenia) are not included. AGNOSIA is a general term for a loss of ability to recognize objects, people, sounds, shapes, or smells; that is, the inability to attach appropriate meaning to objective sense-data. It usually is used when the primary sense organ involved is not impaired. APHASIA is a general term relating to a loss of language ability. APRAXIA is a general term for disorders of practice. These conditions are usually caused by brain injury due to trauma, stroke and/or tumor. Many of these terms have two synonymous forms that differ in whether the word starts with a- or with dys- such as alexia and dyslexia. Here the a- form is usually defined and the other is noted as syn:, except when the dys- form is the more common usage. (If you cannot find a term in one of these forms, look for it in the other. All other synonyms are defined in both forms.) Sources: These definitions are paraphrased from definitions in a large number or print and online dictionaries. Thus this list is not meant to be considered my own, but rather is a compilation. Note: When a word appears in italics, that indicates it is defined elsewhere in this list. | brain injury, trauma, stroke, tumor, brain tumor, developmental deficit, brain, central nervous system, definition, craniocerebral trauma, agnosia, aphasia, apraxia, lexicon | has parent organization: University of Colorado; Colorado; USA | nlx_144393 | SCR_005336 | AGNOSIA APHASIA APRAXIA Related Terms for Cognitive Behavioral Neurological Disorders | 2026-02-17 10:00:32 | 0 | ||||||||
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SBIA Resource Report Resource Website 1+ mentions |
SBIA (RRID:SCR_013628) | SBIA | access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher. | effect, alzheimer's, analysis, anatomical, biomedical, biophysical, brain, cancer, breast cancer, cardiac, classification, clinical, computer, deformation, dimensional, disease, method, model, mouse, organ, pattern, prostate, registration, schizophrenia, segmentation, statistical analysis, study, treatment, image | has parent organization: University of Pennsylvania; Philadelphia; USA | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-33052 | SCR_013628 | The Section for Biomedical Image Analysis, Section for Biomedical Image Analysis | 2026-02-17 10:02:01 | 4 | |||||||
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McConnell Brain Imaging Center Resource Report Resource Website 100+ mentions |
McConnell Brain Imaging Center (RRID:SCR_008364) | BIC | data or information resource, portal, organization portal | Center dedicated to understanding and treatment of neurological diseases by creating and using imaging methods to study human nervous system. Dedicated to research imaging of human brain. Brain structure is imaged using anatomical Magnetic Resonance Imaging (aMRI) while brain physiology is imaged using Positron Emission Tomography (PET), Magnetic Resonance Spectroscopy (MRS), functional MRI (fMRI) and magnetoencephalography (MEG). BIC maintains linkages with clinical, clinical research and basic research communities within Montreal Neurological Institute (MNI), McGill University and has collaborations across Quebec, Canada, USA and internationally. | emission, engineering, environment, fmri, functional mri, 3-dimensional, amri, anatomical, biomedical, brain, chemistry, clinical, computational, computer science, disease, disorder, human, imaging, magnetic, magnetoencephalography, medical, mri, mrs, nervous system, neurological, neurology, neuroscience, neurosurgery, pet, physics, physiology, positron, psychiatric, psychology, research, resonance, scanner, software, spectroscopy, spectrum, technology, tomography, treatment, neuroimaging, meg, atlas, database, data visualization software, data analysis software, data processing software |
is related to: MINC/Atlases has parent organization: McGill University; Montreal; Canada is parent organization of: MINC Example files is parent organization of: MINC is parent organization of: MNI N3 is parent organization of: McConnell Brain Imaging Center MNI Macaque Atlas is parent organization of: McConnell Brain Imaging Center MNI Rhesus Macaque Atlas is parent organization of: McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas is parent organization of: NIHPD Objective 1 atlases (4.5 - 18.5y) is parent organization of: NIHPD Objective 2 atlases (birth - 4.5 years) is parent organization of: ICBM 152 Nonlinear atlases version 2009 |
McConnell Family Foundation | nif-0000-25551 | https://www.mcgill.ca/bic/resources/brain-atlases/ovine-brain-atlas https://www.mcgill.ca/bic/resources/brain-atlases/human https://www.mcgill.ca/bic/resources/brain-atlases/non-human-primate |
SCR_008364 | McConnell Brain Imaging Center, McConnell Brain Imaging Centre, BIC | 2026-02-17 10:01:21 | 129 | ||||||
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Brainvox Resource Report Resource Website 1+ mentions |
Brainvox (RRID:SCR_009448) | image analysis software, software application, data processing software, software resource | An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997). | magnetic resonance, neuroanatomical analysis, software package, 3d, interactive, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
PMID:9038281 | Available for download | nlx_155592 | SCR_009448 | 2026-02-17 10:01:29 | 1 | ||||||||
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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 | data or information resource, reference atlas, atlas | 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 | 2026-02-17 10:01:18 | 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) | data or information resource, reference atlas, atlas | 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) | 2026-02-17 10:01:10 | 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 | data or information resource, reference atlas, atlas | 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 | 2026-02-17 10:01:24 | 1 | |||||||
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BROCCOLI Resource Report Resource Website 10+ mentions |
BROCCOLI (RRID:SCR_014093) | image analysis software, software application, data processing software, 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 | 2026-02-17 10:02:05 | 21 | |||||||||
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BraTS Resource Report Resource Website 1+ mentions |
BraTS (RRID:SCR_016214) | data or information resource, portal, organization portal | 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 | 2026-02-17 10:02:59 | 7 | |||||||||||
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BIDS Validator Resource Report Resource Website 10+ mentions |
BIDS Validator (RRID:SCR_017255) | software application, data processing software, 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 | 2026-02-17 10:03:33 | 20 | ||||||
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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 | software application, data processing software, 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 | 2026-02-17 10:02:52 | 28 | ||||||||
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Mononucleotide Repeat Frameshift Portal Resource Report Resource Website |
Mononucleotide Repeat Frameshift Portal (RRID:SCR_021125) | MORF | data or information resource, portal, organization portal | 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 | 2026-02-17 10:03:57 | 0 | |||||||
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MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, web service, software resource | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://meshview-for-brain-atlases.readthedocs.io https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases |
SCR_017222 | MeshView for brain atlases | 2026-02-17 10:03:33 | 11 | ||||||
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Neuroreader Resource Report Resource Website 10+ mentions |
Neuroreader (RRID:SCR_017309) | NeuroreaderTM | image processing software, software application, data processing software, software resource | Software application as image segmentation tool. Brain volumetry assessment software. Processes MRI scans and provides self explanatory patient report with total brain volume, hippocampal volume and volumetric data on key segments of brain measured against healthy database. | Brain, volumetry, assessment | is affiliated with: Brainreader | PMID:26484924 | Restricted | https://brainreader.net/p/product/neuroreader | SCR_017309 | Neuro Reader, Neuroreader | 2026-02-17 10:03:33 | 11 |
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