Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates
The standard anatomical brain template provides a common space and coordinate system for visualizing and analyzing neuroimaging data from large cohorts of subjects. Previous templates and atlases for the common marmoset brain were either based on data from a single individual or lacked essential fun...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-02-01
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| Series: | NeuroImage |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1053811920311058 |
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| author | Cirong Liu Cecil Chern-Chyi Yen Diego Szczupak Xiaoguang Tian Daniel Glen Afonso C. Silva |
| author_facet | Cirong Liu Cecil Chern-Chyi Yen Diego Szczupak Xiaoguang Tian Daniel Glen Afonso C. Silva |
| author_sort | Cirong Liu |
| collection | DOAJ |
| description | The standard anatomical brain template provides a common space and coordinate system for visualizing and analyzing neuroimaging data from large cohorts of subjects. Previous templates and atlases for the common marmoset brain were either based on data from a single individual or lacked essential functionalities for neuroimaging analysis. Here, we present new population-based in-vivo standard templates and tools derived from multi-modal data of 27 marmosets, including multiple types of T1w and T2w contrast images, DTI contrasts, and large field-of-view MRI and CT images. We performed multi-atlas labeling of anatomical structures on the new templates and constructed highly accurate tissue-type segmentation maps to facilitate volumetric studies. We built fully featured brain surfaces and cortical flat maps to facilitate 3D visualization and surface-based analyses, which are compatible with most surface analyzing tools, including FreeSurfer, AFNI/SUMA, and the Connectome Workbench. Analysis of the MRI and CT datasets revealed significant variations in brain shapes, sizes, and regional volumes of brain structures, highlighting substantial individual variabilities in the marmoset population. Thus, our population-based template and associated tools provide a versatile analysis platform and standard coordinate system for a wide range of MRI and connectome studies of common marmosets. These new template tools comprise version 3 of our Marmoset Brain Mapping Project and are publicly available via marmosetbrainmapping.org/v3.html. |
| first_indexed | 2024-12-20T09:11:32Z |
| format | Article |
| id | doaj.art-0d8b457af2d6454da1dee6c2a8648886 |
| institution | Directory Open Access Journal |
| issn | 1095-9572 |
| language | English |
| last_indexed | 2024-12-20T09:11:32Z |
| publishDate | 2021-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | NeuroImage |
| spelling | doaj.art-0d8b457af2d6454da1dee6c2a86488862022-12-21T19:45:32ZengElsevierNeuroImage1095-95722021-02-01226117620Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templatesCirong Liu0Cecil Chern-Chyi Yen1Diego Szczupak2Xiaoguang Tian3Daniel Glen4Afonso C. Silva5Department of Neurobiology, University of Pittsburgh Brain Institute, 3501 Fifth Avenue, 6065 Biomedical Science Tower 3, Pittsburgh PA, USA; Cerebral Microcirculation Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, ChinaCerebral Microcirculation Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USADepartment of Neurobiology, University of Pittsburgh Brain Institute, 3501 Fifth Avenue, 6065 Biomedical Science Tower 3, Pittsburgh PA, USA; Cerebral Microcirculation Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USADepartment of Neurobiology, University of Pittsburgh Brain Institute, 3501 Fifth Avenue, 6065 Biomedical Science Tower 3, Pittsburgh PA, USA; Cerebral Microcirculation Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USAScientific and Statistical Computing Core, National Institute of Mental Health, National Institutes of Health (NIMH/NIH), Bethesda, MD, USADepartment of Neurobiology, University of Pittsburgh Brain Institute, 3501 Fifth Avenue, 6065 Biomedical Science Tower 3, Pittsburgh PA, USA; Cerebral Microcirculation Section, Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Corresponding author at: Department of Neurobiology, University of Pittsburgh Brain Institute, 3501 Fifth Avenue, 6065 Biomedical Science Tower 3, Pittsburgh PA, USA.The standard anatomical brain template provides a common space and coordinate system for visualizing and analyzing neuroimaging data from large cohorts of subjects. Previous templates and atlases for the common marmoset brain were either based on data from a single individual or lacked essential functionalities for neuroimaging analysis. Here, we present new population-based in-vivo standard templates and tools derived from multi-modal data of 27 marmosets, including multiple types of T1w and T2w contrast images, DTI contrasts, and large field-of-view MRI and CT images. We performed multi-atlas labeling of anatomical structures on the new templates and constructed highly accurate tissue-type segmentation maps to facilitate volumetric studies. We built fully featured brain surfaces and cortical flat maps to facilitate 3D visualization and surface-based analyses, which are compatible with most surface analyzing tools, including FreeSurfer, AFNI/SUMA, and the Connectome Workbench. Analysis of the MRI and CT datasets revealed significant variations in brain shapes, sizes, and regional volumes of brain structures, highlighting substantial individual variabilities in the marmoset population. Thus, our population-based template and associated tools provide a versatile analysis platform and standard coordinate system for a wide range of MRI and connectome studies of common marmosets. These new template tools comprise version 3 of our Marmoset Brain Mapping Project and are publicly available via marmosetbrainmapping.org/v3.html.http://www.sciencedirect.com/science/article/pii/S1053811920311058Magnetic resonance imagingDiffusion tensor imagingComputed tomographyCallithrix jacchusPopulation templatesBrain surfaces |
| spellingShingle | Cirong Liu Cecil Chern-Chyi Yen Diego Szczupak Xiaoguang Tian Daniel Glen Afonso C. Silva Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates NeuroImage Magnetic resonance imaging Diffusion tensor imaging Computed tomography Callithrix jacchus Population templates Brain surfaces |
| title | Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates |
| title_full | Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates |
| title_fullStr | Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates |
| title_full_unstemmed | Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates |
| title_short | Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates |
| title_sort | marmoset brain mapping v3 population multi modal standard volumetric and surface based templates |
| topic | Magnetic resonance imaging Diffusion tensor imaging Computed tomography Callithrix jacchus Population templates Brain surfaces |
| url | http://www.sciencedirect.com/science/article/pii/S1053811920311058 |
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