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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Rat Brain Atlas of Paxinos and Watson Resource Report Resource Website 10+ mentions |
Rat Brain Atlas of Paxinos and Watson (RRID:SCR_006369) | Rat Brain Atlas of Paxinos & Watson | atlas, data or information resource, reference atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 27,2025. Compact 3rd edition of The Rat Brain Atlas of Paxinos & Watson published in 1997, it is the most widely used stereotaxic reference system for rat brain. The illustrations and nomenclature of the atlas have become standard tools used by almost all research neuroscientists who deal with anatomy, physiology, or function. It has been subsequently updated, with the 6th edition being the most recent. The 3rd edition is the most recent one available online for free. The program runs in Adobe Acrobat Reader. | rat, stereotaxic coordinate, brain, neuroanatomy | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152120 | SCR_006369 | Rat Brain Atlas - Paxinos & Watson, Rat Brain in Stereotaxic Coordinates | 2026-09-19 12:55:55 | 20 | ||||||||
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McConnell Brain Imaging Center MNI Macaque Atlas Resource Report Resource Website 1+ mentions |
McConnell Brain Imaging Center MNI Macaque Atlas (RRID:SCR_005265) | atlas, data or information resource, reference atlas | A reference atlas of standard 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 macaque monkeys and studies. We have used MRI volumes from a group of 25 normal adult macaque monkeys (18 Macaca fascicularis, 7 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 macaque brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the MNI 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. | macaque, brain, early adult, template, atlas application, minc, minc2, magnetic resonance, nifti, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McConnell Brain Imaging Center |
PMID:21256229 | Free | nlx_144292 | http://www.nitrc.org/projects/mniatlas | SCR_005265 | MNI Macaque Atlas, BIC MNI Macaque Atlas | 2026-09-19 12:55:54 | 2 | ||||||
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NeuroSynth Resource Report Resource Website 1000+ mentions |
NeuroSynth (RRID:SCR_006798) | Neurosynth | data or information resource, database, software resource, source code | Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image. | activation foci, magnetic resonance imaging assay, brain, human, fmri, neuroimaging, python, image, functional neuroimaging, FASEB list |
is used by: NeuroVault is used by: NIF Data Federation is listed by: GitHub is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brainspell has parent organization: University of Texas at Austin; Texas; USA |
NIMH R01MH096906 | PMID:21706013 | Neurosynth Automated Coordinate Extraction (ACE) tools under, Open unspecified license, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552, Software is, Free, Copyright and permission notice required | nlx_55906 | http://www.nitrc.org/projects/neurosynth, https://github.com/tyarkoni/neurosynth | SCR_006798 | Neurosynth.org | 2026-09-19 12:55:56 | 1340 | ||||
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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, organization portal, 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 | 2026-09-19 12:55:57 | 133 | ||||||
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UAB Comprehensive Neuroscience Center Resource Report Resource Website |
UAB Comprehensive Neuroscience Center (RRID:SCR_007195) | data or information resource, organization portal, portal | The overall mission of the Comprehensive Neuroscience Center (CNC) is to promote and support interdisciplinary neuroscience research, clinical care and education at UAB. Despite significant advances over the last 15 years in understanding many basic neurological processes, development of more effective treatments for neurological and psychiatric diseases have been identified as the largest and fastest growing unmet medical need in this country. The institutions that can most rapidly and creatively establish the necessary neuroscience initiatives to facilitate the translation of basic research discoveries into effective therapies will be positioned to lead neurological and psychiatric disease research into the future. The Center integrates a variety of disciplines, including neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, and biomedical engineering. Faculty from the Schools of Medicine, Optometry, Social and Behavioral Sciences, Dentistry, Engineering, Health Professions, and Public Health are affiliated with the Center. The need to address neuroscience research is great: one in three Americans are affected by nervous system diseases including brain and spinal cord injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, and autism. The burden of these diseases has an estimated economic cost of 500 billion per year in the United States. Center Research: The CNC serves as a vital center for neuroscience research at UAB and oversees six thematic programs of investigation: neurodevelopment and neurogenetics, neurodegeneration and experimental therapeutics, neuroregeneration and plasticity, behavioral and cognitive health, glial biology in medicine, and neuroimaging. The CNC helps coordinate the efforts of multiple neuroscience related centers at UAB, such as the Center for Glial Biology in Medicine, the Evelyn F. McKnight Brain Institute, the Civitan International Research Center, and the Alzheimers Disease Research Center. By interacting directly with these centers and establishing coalitions of centers and neuroscience subdisciplines, the CNC aids the UAB neuroscience community in meeting the challenges of modern neuroscience investigation. The CNC builds on other recent advances in neuroscience at UAB, including an 8.6 million grant from the National Institutes of Health to establish the Alabama Neuroscience Blueprint Core Center Facility awarded in September 2006. The Neuroscience Blueprint establishes research infrastructure on campus that is shared by investigators from institutions across Alabama and the Southeast. UAB has also added dynamic new leadership in the neuroscience fields including the following new chairs: Ray L. Watts, MD, Neurology (from Emory University); David Sweatt, PhD, Neurobiology (from Baylor College of Medicine); and James Meador-Woodruff, MD, Psychiatry (from the University of Michigan). | core facility, neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, biomedical engineering, nervous system, diseases, brain, spinal cord, injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, autism, neuroscience, neurogenetics, neuroimaging, alzheimer | has parent organization: University of Alabama; Alabama; USA | nif-0000-00652 | SCR_007195 | University Of Alabama at Birmingham, UAB Comprehensive Neuroscience Center, CNC | 2026-09-19 12:55:56 | 0 | |||||||||
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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 | atlas, data or information resource, reference 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 | 2026-09-19 12:55:58 | 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) | atlas, data or information resource, reference 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) | 2026-09-19 12:55:58 | 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 | atlas, data or information resource, reference 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 | 2026-09-19 12:55:58 | 1 | |||||||
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Virtual Atlas of the Honeybee Brain Resource Report Resource Website 1+ mentions |
Virtual Atlas of the Honeybee Brain (RRID:SCR_007133) | Virtual Atlas of the Honeybee Brain | atlas, data or information resource, reference atlas | Standard brain atlas of the honeybee presented as an interactive three-dimensional surface model with integrated neuron and neuronal tracts. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The Honeybee, Apis mellifera has been studied extensively with respect to its sensory and neural capacities in navigation, communication, visual and olfactory learning and memory processing. The goal is to integrate the entirety of information into a Virtual Atlas of the Honeybee Brain. This common spatial reference map will potentiate the representation of structural and functional data obtained in different experiments and from different individuals. | anatomy, honeybee, brain, insect, insecta, normal, antennal lobe, olfactory | has parent organization: Free University of Berlin; Berlin; Germany | BMBF | PMID:16175557 | nif-0000-00089 | SCR_007133 | 2026-09-19 12:55:56 | 6 | |||||||
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Brainvox Resource Report Resource Website 1+ mentions |
Brainvox (RRID:SCR_009448) | data processing software, image analysis software, software application, 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 | 2026-09-19 12:55:59 | 1 | ||||||||
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Brain.io Resource Report Resource Website |
Brain.io (RRID:SCR_014527) | data or information resource, portal, project portal | 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 | 2026-09-19 12:56:03 | 0 | |||||||||||
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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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Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data analysis software, data processing software, software application, software resource, source code | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/, https://markmikkelsen.github.io/Gannet-docs/index.html | http://www.gabamrs.com/about | SCR_016049 | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-09-19 12:53:16 | 167 | ||||||||
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MRTool Resource Report Resource Website 10+ mentions |
MRTool (RRID:SCR_015956) | data or information resource, portal, topical portal | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-09-19 12:53:14 | 14 | |||||||||
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Marmoset Brain Connectivity Atlas Resource Report Resource Website 10+ mentions |
Marmoset Brain Connectivity Atlas (RRID:SCR_015964) | atlas, data or information resource, data repository, database, service resource, storage service resource | Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex. | cortex, marmoset, monkey, cerebral, brain, architecture, primate |
has parent organization: Monash University; Melbourne; Australia has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland works with: Nencki-Monash template |
Australian Research Council CE140100007; Australian Research Council DP140101968; European Regional Development Fund ; International Neuroinformatics Coordinating Facility ; NIDA R01 DA036400; NIMH R01 MH087988 |
DOI:10.1038/s41467-020-14858-0 PMID:27099164 |
Free, Freely available | http://marmoset.braincircuits.org, http://analysis.marmosetbrain.org | SCR_015964 | Marmoset Monkey Cerebral Cortex Connectivity Atlas | 2026-09-19 12:53:15 | 26 | ||||||
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NeuroXM Brain Science Suite Resource Report Resource Website |
NeuroXM Brain Science Suite (RRID:SCR_016372) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data. | semantic, data, graph, neuroscience, neuroanatomy, ontology, circuitry, pathway, multimodal, brain | Commercially available | SCR_016372 | Brain Science Suite, NeuroXM, NeuroXM Suite | 2026-09-19 12:53:22 | 0 | ||||||||||
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Colour maps for brain imaging Resource Report Resource Website 1+ mentions |
Colour maps for brain imaging (RRID:SCR_016715) | data processing software, data visualization software, image analysis software, software application, software resource | Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging. | perceptually, uniform, color, map, brain, data, imaging |
is related to: MRIcron is related to: MATLAB has parent organization: University of Western Australia; Perth; Australia |
Free, Available for download, Freely available | SCR_016715 | Colour maps, brain_colours, colour maps, brain colours, Brain colours, colour maps for brain imaging, Colour maps for brain imaging | 2026-09-19 12:53:28 | 1 | |||||||||
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ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | data analysis software, data processing software, software application, software resource | Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders. | nonparametric, statistical, test, compare, clustering, structure, functional, brain, network, magnetic, resonance, imaging, data, fMRI, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: CRAN |
CAPES and CNPq Fellowships ; Ciência sem Fronteiras Fellowship ; NAP eScience ; Pew Latin American Fellowship ; State of São Paulo Research Foundation |
PMID:28174516 | Free, Available for download, Freely available | biotools:anocva | https://bio.tools/anocva | SCR_016719 | ANalysis Of Cluster VAriability, Analysis of Cluster Variability | 2026-09-19 12:53:28 | 0 | ||||
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MouseLight Project Resource Report Resource Website 10+ mentions |
MouseLight Project (RRID:SCR_016668) | analysis service resource, data access protocol, data analysis service, data or information resource, database, portal, production service resource, service resource, software resource, web service | Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain. | neuronal, reconstruction, connectomics, projectomics, brain, tissue, image, dataset, mouse, axonal, arbor, individual, neuron |
is related to: Allen Institute for Brain Science has parent organization: Janelia Research provides: MouseLight Neuron Browser |
Free, Freely available, Tutorial available, Acknowledgement required, Registration required | http://mouselight.janelia.org/ | SCR_016668 | MouseLight, The Mouse Light Project, Janelia MouseLight project, Mouse Light Project, Mouse Light, MouseLight Project | 2026-09-19 12:53:27 | 12 | ||||||||
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rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data analysis software, data processing software, software application, software resource | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-09-19 12:53:26 | 1 |
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