In vivo localization of cortical areas using a 3D computerized atlas of the marmoset brain View Full Text


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Article Info

DATE

2019-04-08

AUTHORS

Laurent Risser, Amirouche Sadoun, Muriel Mescam, Kuzma Strelnikov, Sandra Lebreton, Samuel Boucher, Pascal Girard, Nathalie Vayssière, Marcello G. P. Rosa, Caroline Fonta

ABSTRACT

We created a volumetric template of the marmoset (Callithrix jacchus) brain, which enables localization of the cortical areas defined in the Paxinos et al. (The marmoset brain in stereotaxic coordinates. Elsevier Academic Press, Cambridge, 2012) marmoset brain atlas, as well as seven broader cortical regions (occipital, temporal, parietal, prefrontal, motor, limbic, insular), different brain compartments (white matter, gray matter, cerebro-spinal fluid including ventricular spaces), and various other structures (brain stem, cerebellum, olfactory bulb, hippocampus). The template was designed from T1-weighted MR images acquired using a 3 T MRI scanner. It was based on a single fully segmented marmoset brain image, which was transported onto the mean of 13 adult marmoset brain images using a diffeomorphic strategy that fully preserves the brain topology. In addition, we offer an automatic segmentation pipeline which fully exploits the proposed template. The segmentation pipeline was quantitatively assessed by comparing the results of manual and automated segmentations. An associated program, written in Python, can be used from a command-line interface, or used interactively as a module of the 3DSlicer software. This program can be applied to the analysis of multimodal images, to map specific cortical areas in lesions or to define the seeds for further tractography analyses. More... »

PAGES

1957-1969

References to SciGraph publications

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  • 2008. Symmetric Log-Domain Diffeomorphic Registration: A Demons-Based Approach in MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION – MICCAI 2008
  • 2015-11-03. Cognitive impairment in a young marmoset reveals lateral ventriculomegaly and a mild hippocampal atrophy: a case report in SCIENTIFIC REPORTS
  • 2008. The Marmoset Brain in Stereotaxic Coordinates in NONE
  • 2015-08-12. Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool in BMC MEDICAL IMAGING
  • 2011-08-03. Diffeomorphic 3D Image Registration via Geodesic Shooting Using an Efficient Adjoint Calculation in INTERNATIONAL JOURNAL OF COMPUTER VISION
  • 2015-02-17. The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content in NEUROINFORMATICS
  • 2014-07-20. The common marmoset genome provides insight into primate biology and evolution in NATURE GENETICS
  • 2013-08-14. 3D Brain Atlas Reconstructor Service—Online Repository of Three-Dimensional Models of Brain Structures in NEUROINFORMATICS
  • 2018-02-13. The Brain/MINDS 3D digital marmoset brain atlas in SCIENTIFIC DATA
  • 2017-09-29. Managing competing goals — a key role for the frontopolar cortex in NATURE REVIEWS NEUROSCIENCE
  • 2012-01-07. Common Atlas Format and 3D Brain Atlas Reconstructor: Infrastructure for Constructing 3D Brain Atlases in NEUROINFORMATICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00429-019-01869-x

    DOI

    http://dx.doi.org/10.1007/s00429-019-01869-x

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1113300963

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30963231


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