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

  • Laurent Risser
  • Amirouche Sadoun
  • Muriel Mescam
  • Kuzma Strelnikov
  • Sandra Lebreton
  • Samuel Boucher
  • Pascal Girard
  • Nathalie Vayssière
  • Marcello G. P. RosaEmail author
  • Caroline FontaEmail author
Methods Paper


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.


MRI New world monkey Mapping Template Cortex 



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.


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).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Research involving animals/ethical approval

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).

Supplementary material

429_2019_1869_MOESM1_ESM.docx (1009 kb)
Supplementary material 1 (DOCX 1009 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS IMTToulouse Cedex 9France
  2. 2.Centre de recherche Cerveau et Cognition (CerCo), Université de Toulouse UPS, CNRS, UMR 5549, CHU PurpanToulouse Cedex 3France
  3. 3.INSERMToulouseFrance
  4. 4.Department of Physiology, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
  5. 5.Australian Research Council, Centre of Excellence for Integrative Brain FunctionMonash University NodeClaytonAustralia

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