Atlas-based analysis of human brainstem anatomy as revealed by gradient-echo T2*-weighted MR imaging at 7T

Abstract

Introduction Spatial MR image resolution improved drastically with appearance of ultra-high field MR systems. Moreover, new contrasts based on iron concentration in deep nuclei emerged. Iron deposition results in signal drop in T2*-weighted images on high-field systems which helps the segmentation of some mesencephalon structures (e.g. substantia nigra, red nucleus, and subthalamic nucleus) that cannot be well delineated at lower field. This is of a great interest in Parkinson’s disease studies where pathological alterations of the aforementioned structures are observed [1, 2]. Nonetheless, for a variant of Parkinson disease some other smaller structures of the brainstem are also involved (e.g. pedunculopontine nucleus PPN) but they cannot be distinguished even with high resolution images at 7T. We have thus analyzed a gradient echo T2-weighted MR acquisition with the help of two different atlases: 1) a 3D histological [3] and deformable [4] atlas, which comprises several nuclei and fiber bundles of the mesencephalon, 2) a printed histological atlas of the entire brainstem [5] that we have numerized and reconstructed for this study.