1. A method for segmenting an image, comprising: registering an annotated template image to an acquired reference image using only rigid transformations to define a transformation function relating the annotated template image to the acquired reference image; refining the defined transformation function by registering the annotated template image to the acquired reference image using only the rigid transformations and scaling in which scale is held equal for x, y, and z axes; further refining the refined transformation function by registering the annotated template image to the acquired reference image using only multi-affine transformations, wherein the step of further refining using only multi-affine transformations is divided into multiple registration steps wherein at each successive step thereof, registration is iterated by including additional transformation centers such that a number of transformation centers used during each successive registration step progressively increases; and still further refining the twice refined transformation function by registering the annotated template image to the acquired reference image using deformation transformations.