Abstract: The invention provides a hierarchical method that is based on multi-scale computation and motion-tracking algorithms to register images. A hierarchical registration algorithm is used to address extrinsic and intrinsic variations. In particular, a global similarity transformation is applied to align anatomical structures in a global manner. Next, a local similarity transformation is applied to fine-tune and adjust internal details. The registration output provides the input necessary for other automated computations, such as volume and size comparisons and measurements.