Semi-automatic segmentation of brain sub-cortical structures from ultra high-field MRI


Volumetric segmentation of sub-cortical structures such as the basal ganglia and thalamus is necessary for non-invasive diagnosis and neurosurgery planning. This is a challenging problem due in part to limited boundary information between structures, similar intensity profiles across the different structures, and low contrast data.

This work presents a semi-automatic segmentation system exploiting the superior image quality of ultra-high field (7 Tesla) MRI. The proposed approach utilizes the complementary edge information in the multiple structural MRI modalities. It combines optimally selected two modalities from susceptibility-weighted, T2-weighted, and diffusion MRI, and introduces a tailored new edge indicator function. In addition to this, we employ prior shape and configuration knowledge of the sub-cortical structures in order to guide the evolution of geometric active surfaces. Neighboring structures are segmented iteratively, constraining over-segmentation at their borders with a non-overlapping penalty. Several experiments with data acquired on a 7T MRI scanner demonstrate the feasibility and power of the approach for the segmentation of basal ganglia components critical for neurosurgery applications such as deep brain stimulation surgery.


Jinyoung Kim , Department of Electrical and Computer Engineering


Imaging and the Brain