Automatic segmentation of internal structures of the brain in MR images using a tandem of affine and non-rigid registration of an anatomical brain atlas

In the study of many neurological pathologies, the accurate quantization of the white matter (WM) and gray matter (GM) volumes of the brain is essential. Moreover, regional volume calculations may bring even more useful diagnostic information. In this paper, we present therefore the segmentation of internal structures of the brain for further regional WM and GM volume quantization. A priori information about the brain anatomy is included in the segmentation process by the registration of the patient MR images with a computerized brain atlas. We propose here the combination of a global affine transformation used to initialize key boundary surfaces (lateral ventricles and cortical surfaces) of both images with a local free-form transformation based on an optical flow algorithm. We apply this technique to segment the cerebellum and the cerebral trunk in order to exclude them from our WM and GM volume quantization. Validation has been conducted on a large number of images, showing excellent results.