Thesis defense – Elise Cosenza

Venue: BBS

Thesis defended in french

Elise Cosenza

Team: Neurofunctional imaging group (GIN)
IMN

Thesis directed by Laurent Petit

Title

Development of diffusion MRI and tractography of brain white matter fibers in the small animal at 7 Tesla

Abstract

The study of brain connectivity in mice is a major challenge for preclinical research. Although the mouse brain is anatomically simpler than the human brain, it remains a complex system. Its anatomical organisation is now well described and segmented thanks to the many atlases available, but the connections between the different structures are still poorly understood. White matter, formed by bundles of axons connecting brain regions, constitutes a network whose characterisation is essential to better understand the overall functioning of the murine brain.

Diffusion magnetic resonance imaging (dMRI) has established itself as an essential method for non-invasive brain studies. It is based on measuring the movement of water molecules and allows indirect deduction of tissue architecture and brain connectivity, given that the brain is composed of more than 80% water. Using this data, tractography can be used to highlight all the brain’s connections. Although widely developed in humans and enhanced by numerous processing tools, dMRI and tractography have several limitations due to their indirect nature. To validate and refine the results, fMRI and tractography must be combined with complementary, sometimes invasive methods that provide essential “ground truth” data.

Methodologically, diffusion MRI protocols were optimised on ex vivo mouse brains, enabling reliable, quantitative diffusion metrics to be obtained across all brain regions. An automated tool for processing dMRI data, incorporating quality controls and artefact corrections, was developed to generate these metrics and reconstruct a complete tractogram of white matter connectivity. Finally, the validity of these results was confirmed by directly comparing the tractograms with histological data, using tools dedicated to coupling MRI and histology.

This work paves the way for better characterisation of brain connectivity networks in preclinical animal models. These advances offer major prospects for understanding how the brain works and its plasticity, as well as for studying mouse models of neurological disorders.

Key words

MRI; Tratography; Brain; White Matter; Mice; Diffusion

Publication

“MRI R2* captures inflammation in disconnected brain structures after stroke: a translational study”

An optimised multi-shot EPI protocol for ex vivo mouse brain diffusion MRI with Gd-DOTA contrast enhancement (submitted) 

Jury

• Dr. Emmanuel Caruyer, CR, IRISA – Rennes, Rapporteur
• Pr. Ileana Jelescu, Assistant professor, Lausanne University Hospital et University of Lausanne – Lausanne (Suisse), Rapporteure
• Dr. Angèle Viola, DR, Centre de Résonance Magnétique Biologique et Médicale – Marseille, Examinatrice
• Pr. Maxime Descoteaux, Professeur titulaire, Sherbrooke Connectivity Imaging Laboratory – Sherbrooke (Canada), Invité
• Dr. Sylvain Miraux, DR, Centre de Résonance Magnétique des Systèmes Biologiques – Bordeaux, Invité

• Place
  BBS
  
• Dates
  On 5 December 2025 at 15:00