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CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques

Claude Lepage, View ORCID ProfileKonrad Wagstyl, View ORCID ProfileBenjamin Jung, View ORCID ProfileJakob Seidlitz, View ORCID ProfileCaleb Sponheim, View ORCID ProfileLeslie Ungerleider, View ORCID ProfileXindi Wang, View ORCID ProfileAlan C. Evans, View ORCID ProfileAdam Messinger
doi: https://doi.org/10.1101/2020.08.04.237149
Claude Lepage
aMontreal Neurological Institute (MNI), McGill University, Montreal, Canada
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Konrad Wagstyl
aMontreal Neurological Institute (MNI), McGill University, Montreal, Canada
bWellcome Centre for Human Neuroimaging, University College London, London, UK
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Benjamin Jung
cLaboratory of Brain and Cognition, National Institute of Mental Health, Bethesda MD USA
dDepartment of Neuroscience, Brown University, Providence RI USA
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Jakob Seidlitz
eDepartment of Child and Adolescent Psychiatry and Behavioral Science, Children’s Hospital of Philadelphia, Philadelphia PA USA
fDepartment of Psychiatry, University of Pennsylvania, Philadelphia PA USA
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Caleb Sponheim
gDepartment of Organismal Biology and Anatomy, University of Chicago, Chicago IL USA
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Leslie Ungerleider
cLaboratory of Brain and Cognition, National Institute of Mental Health, Bethesda MD USA
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  • ORCID record for Leslie Ungerleider
Xindi Wang
aMontreal Neurological Institute (MNI), McGill University, Montreal, Canada
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Alan C. Evans
aMontreal Neurological Institute (MNI), McGill University, Montreal, Canada
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Adam Messinger
cLaboratory of Brain and Cognition, National Institute of Mental Health, Bethesda MD USA
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  • For correspondence: messinga@mail.nih.gov
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Abstract

The MNI CIVET pipeline for automated extraction of cortical surfaces and evaluation of cortical thickness from in-vivo human MRI has been extended for processing macaque brains. Processing is performed based on the NIMH Macaque Template (NMT), as the reference template, with the anatomical parcellation of the surface following the D99 and CHARM atlases. The modifications needed to adapt CIVET to the macaque brain are detailed. Results have been obtained using CIVET-macaque to process the anatomical scans of the 31 macaques used to generate the NMT and another 95 macaques from the PRIME-DE initiative. It is anticipated that the open usage of CIVET-macaque will promote collaborative efforts in data collection and processing, sharing, and automated analyses from which the non-human primate brain imaging field will advance.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 05, 2020.
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CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques
Claude Lepage, Konrad Wagstyl, Benjamin Jung, Jakob Seidlitz, Caleb Sponheim, Leslie Ungerleider, Xindi Wang, Alan C. Evans, Adam Messinger
bioRxiv 2020.08.04.237149; doi: https://doi.org/10.1101/2020.08.04.237149
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CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques
Claude Lepage, Konrad Wagstyl, Benjamin Jung, Jakob Seidlitz, Caleb Sponheim, Leslie Ungerleider, Xindi Wang, Alan C. Evans, Adam Messinger
bioRxiv 2020.08.04.237149; doi: https://doi.org/10.1101/2020.08.04.237149

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