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

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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.

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Acknowledgements

We would like to thank Tristan Chaplin and Piotr Majka for generating the 3D map of cytoarchitectural areas of the marmoset brain derived from the atlas of (Paxinos et al. 2012). Our gratitude goes to MRI platform (INSERM UMR1214) for their priceless assistance. We also thank the staff of the CerCo animal rearing facilities and Emilie Rapha for their help with animal preparation and monitoring.

Funding

This work was financially supported by the University Paul Sabatier, Toulouse 3 (AO1 MST2I_2013) and the Toulouse Mind and brain Institute (TMBI, AO2015). A.S. Ph.D. was Granted by University Paul Sabatier/Toulouse 3 and Foundation for Medical Research (FDT20160435166). The participation of MGP Rosa was funded by the Australian Research Council’s Centre of Excellence for Integrative Brain function (CE140100007).

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Author notes

  1. Laurent Risser, Amirouche Sadoun and Muriel Mescam have equal contribution.

Authors and Affiliations

  1. Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS IMT, 31062, Toulouse Cedex 9, France

    Laurent Risser & Sandra Lebreton

  2. Centre de recherche Cerveau et Cognition (CerCo), Université de Toulouse UPS, CNRS, UMR 5549, CHU Purpan, Pavillon Baudot, BP 25202, 31052, Toulouse Cedex 3, France

    Amirouche Sadoun, Muriel Mescam, Kuzma Strelnikov, Samuel Boucher, Pascal Girard, Nathalie Vayssière & Caroline Fonta

  3. INSERM, Toulouse, France

    Pascal Girard

  4. Department of Physiology, Biomedicine Discovery Institute, Monash University, 26 Innovation Walk, Clayton, VIC, 3800, Australia

    Marcello G. P. Rosa

  5. Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC, 3800, Australia

    Marcello G. P. Rosa

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  1. Laurent Risser
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Correspondence to Marcello G. P. Rosa or Caroline Fonta.

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All applicable international, national and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted. The project received the regional (MP/03/76/11/12) and the governmental authorization from the MENESR (project 05215.03).

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Risser, L., Sadoun, A., Mescam, M. et al. In vivo localization of cortical areas using a 3D computerized atlas of the marmoset brain. Brain Struct Funct 224, 1957–1969 (2019). https://doi.org/10.1007/s00429-019-01869-x

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