Atlas-based segmentation techniques are often employed to encode anatomical information for the delineation of multiple structures in magnetic resonance images of the brain.

One of the primary challenges of these approaches is to efficiently model qualitative and quantitative anatomical knowledge without introducing a strong bias toward certain anatomical preferences when segmenting new images. Topology can be used to describe the continuity of structures, as well as the relationships between structures, and is often a critical component in cortical surface reconstruction and deformation-based morphometry. I will present methods to incorporate topological atlas information into atlas-based algorithms for the segmentation of brain structures in MRI.