Cortical Surface Segmentation and Topology Correction for 3D Visualization of Brain MR Images

Abstract

Human brain magnetic resonance (MR) images are widely used for the several purposes, such as visualization of the cortical surface, measurement of the cortical thickness, generation and degeneration of the brain, and diagnosis and analysis of disease. In these types of studies, a brain region is extracted from MR images in an important preprocessing step called skull stripping. In general, skull stripping is performed either by manual segmentation or automatic segmentation. However, because manual segmentation has drawbacks, such as the need for trained experts and the laboriousness of the task, automatic skull tripping is generally preferable in large-scale studies. After the skull stripping, we can visualize the brain region, including the cerebrum, the cerebellum, and part of the brain stem. Only the cerebrum volume is needed to visualize the cerebral cortex, so the cerebellum and the brain stem should be removed. By using the cerebellum segment, we can investigate various functional activities of the cerebellum, such as the motor, balance, language, and distance measurement functions. A skull-stripped volume without the cerebellum is then obtained, and the cerebral cortex can be transformed into a sphere or flat map for analysis of the cerebral cortex across populations. However, the cerebrum volume has topological defects, such as tunnels and holes, which prevent the occurrence of homeomorphism when the cerebral cortex is transformed into a sphere or flat map. This thesis proposes a skull-stripping method based on a level set method with a speedup operator and a refinement process. We first extend a conventional 2D level set method to a 3D equation and then apply the speedup operator to reduce the computation load. The speedup operator can improve the propagation speed of zero level surfaces while maintaining a signed distance function. Because the skull-stripped volume includes the cerebrum, the cerebellum, and part of the brain stem, we propose a cerebe...