Atlas-Based Analysis of Human Brainstem Anatomy as Revealed by Gradient-Echo T2 Weighted MR Imaging at 7T

Fabrice Poupon^1,2, Dominique Hasboun³, Linda Marrakchi^1,2, Eric Bardinet⁴, Jean-Franois Mangin^1,2, Irina Kezele^1,2, Sarah Fernandez-Vidal⁵, Kamil Ugurbil⁶, Stphane Lehericy⁷, Cyril Poupon^1,2, Pierre-Franois van de Moortele⁶, Jrme Yelnik⁵

Spatial resolution improved with ultra-high field MR systems, and new contrasts based on iron concentration help the segmentation of some mesencephalon structures which are of interest in Parkinson disease studies. Nonetheless, in a variant of Parkinsons disease, smaller structures of the brainstem are involved. An experienced anatomist explored the brainstem structures by direct identification in a gradient-echo T2-weighted MRI at 7T. This identification was guided by two histological atlases: a 3D histological and deformable atlas of the basal ganglia comprising several structures of the mesencephalon and a numerized and reconstructed version of a printed atlas of the entire brainstem.