GPU-accelerated, gradient-free MI deformable registration for atlas-based MR brain image segmentation

Brain structure segmentation is an important task in many neuroscience and clinical applications. In this paper, we introduce a novel MI-based dense deformable registration method and apply it to the automatic segmentation of detailed brain structures. Together with a multiple atlas fusion strategy, very accurate segmentation results were obtained, as compared with other reported methods in the literature. To make multi-atlas segmentation computationally feasible, we also propose to take advantage of the recent advancements in GPU technology and introduce a GPU-based implementation of the proposed registration method. With GPU acceleration it takes less than 8 minutes to compile a multi-atlas segmentation for each subject even with as many as 17 atlases, which demonstrates that the use of GPUs can greatly facilitate the application of such atlas-based segmentation methods in practice.