Medical imaging

Medical imaging

Keywords: MRI, segmentation, mesh reconstruction.

Abstract: pre and post-operative images like MRI can be modelized as voxel matrices, and a large number of algorithms from discrete geometry can be applied. Extracting a surface from such a description is also an interesting way to modelize the observed anatomical objects (organs, tissues, etc.) and facilitate the usage of geometrical and topological tools. I mainly worked on this approach, generating surfaces from the voxel description, then modifying the surface by integrating expert knowledge, related with geometry or topology, or extracting information to measure properties.

Main activity

I am a permanent member of the ALCoV team, ISIT, Université d'Auvergne, focusing on endoscopic surgery. ALCoV's scientific project brings new tools for surgical gesture training and decision making using virtual reality and for computer vision and augmented reality aided surgery. I am interested in extracting structured mesh from pre-operative images, to enrich the per-operative tools.


  • 2009-2011: Olivier Salvado, Biomedical Imaging Group, Australian eHealth Research Centre, CSIRO
    • I am involved in a FAST project (EGIDE), and I was during one month (August 2010) in Brisbane, working at CSIRO on topological correction of volumic data.
  • 2006-2009: Vincent Barra, LIMOS, UMR CNRS, Université Blaise Pascal
  • 2006: Jean-Jacques Lemaire, ERIM, Université d'Auvergne
  • 2005: Christian Barillot, ViSaGeS, IRISA.


  • Oscar Acosta, Jurgen Fripp, Vincent Dore, Pierrick Bourgeat, Jean-Marie Favreau, Gaël Chételat, Andrea Rueda, Victor L. Villemagne, Cassandra Szoeke, David Ames, Kathryn A. Ellis, Ralph N. Martins, Colin L. Masters, Christopher C. Rowe, Erik Bonner, Florence Gris, Di Xiao, Parnesh Raniga, Vincent Barra, Olivier Salvado Cortical surface mapping using topology correction, partial flattening and 3D shape context-based non-rigid registration for use in quantifying atrophy in Alzheimer's disease. Journal of Neuroscience Methods 205 (1) pp. 96-109. (2011). doi web bibtex
  • J.-M. Favreau Outils pour le pavage de surfaces. (2009). web bibtex
  • J-M Favreau, S. Hemm, C. Nuti, J. Coste, V. Barra, J.-J. Lemaire A Tool for Topographic Analysis of Electrode Contacts in Human Cortical Stimulation. In MMBIA'07. IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis ICCV 2007. Rio de Janeiro, Brazil (October/2007). bibtex
  • J.-M. Favreau Atlas probabiliste des frontières fonctionnelles des aires visuelles. (2005). bibtex
  • J.-M. Favreau, C. Ciofolo, C. Barillot Extraction et étude statistique du sillon calcarin. In MajecSTIC 2005 : Manifestation des Jeunes Chercheurs francophones dans les domaines des STIC . pp. 423-426 . Rennes (2005). web bibtex