A method of verifying a registration of a digital image includes receiving a reference image and a moving image registered to the reference image representing the same object, selecting one or more landmarks in the images, defining a neighborhood in the domain of each image near each selected landmark, extracting feature sets from the neighborhoods for the reference image and the registered moving image, calculating a total quality measure of the registration of the moving image from a distance metric applied to the feature sets extracted from the neighborhoods of the reference image and the registered moving image, comparing the total quality measure to a threshold determined from a reference atlas for the object represented in the image, and determining whether to accept or reject the registration of the moving image based on the comparison result.