An automated process classifies MRI or other medical imaging data as belonging to neurological structures. A training part of the process uses a baseline data set with accompanying classification map, as well as an arbitrary number of training data sets, also with accompanying classification maps. Each training data set is registered to the baseline data set using a warp-based automated registration algorithm. The resulting probability map, mean values and covariance matrices are used to classify structures in an image data set using a maximum likelihood criterion.