1. A method for segmenting a patient image based on an atlas, wherein the steps of, at a processor: performing at least a first and a second rigid registration using a registration method allowing rigid transformations wherein the patient image is registered with at least a first and a second atlas image, respectively, said atlas images being acquired from different atlases comprising one or more segmented regions of interest, said rigid registrations resulting in a rigid registration result for each of the atlas images; determining a degree of similarity for each of the atlas images based on said rigid registration results; selecting an atlas on basis of the determined degree of similarity for each of the atlas images; performing a deformable registration using a registration method allowing non-rigid transformations wherein the patient image is registered with the atlas image of said selected atlas using said rigid registration result for the atlas image of said selected atlas as initialization, said deformable registration resulting in a deformable registration result; segmenting at least one region of interest in the patient image at least partly based on said deformable registration result.