Automated topology correction for human brain segmentation.

We describe a new method to reconstruct human brain structures from 3D magnetic resonance brain images. Our method provides a fully automatic topology correction mechanism, thus avoiding tedious manual correction. Topological correctness is important because it is an essential prerequisite for brain atlas deformation and surface flattening. Our method uses an axis-aligned sweep through the volume to locate handles. Handles are detected by successively constructing and analyzing a directed graph. A multiple local region-growing process is used which simultaneously acts on the foreground and the background to isolate handles and tunnels. The sizes of handles and tunnels are measured, then handles are removed or tunnels filled based on their sizes. This process was used for 256 T1-weighted MR volumes.