A method for segmenting a patient image based on an atlas, characterized by the steps of, at a processor: - performing, for each of at least two atlases, each comprising one or more segmented regions of interest (21, 22, 23, 24, 25), a preparatory registration using a registration method allowing rigid transformations wherein the patient image is registered with a complete atlas image acquired from the atlas, resulting in a preparatory registration result for said complete atlas image which is used as initialization for at least one of the following rigid registration steps; - 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 sub-atlas image (210, 220, 230, 240, 250), respectively, said sub-atlas images being sub-sets of, and derived from, different complete atlas images comprising one or more segmented regions of interest (21, 22, 23, 24, 25), wherein each of said rigid registrations of the patient image with each of said sub-atlas images comprises multiple consecutive registrations where the size of the sub-atlas image is reduced before each subsequent registration, said rigid registrations resulting in a rigid registration result for each of the sub-atlas images; - determining a degree of similarity for each of the sub-atlas images (210, 220, 230, 240, 250) based on said rigid registration results; - selecting an atlas on basis of the determined degree of similarity for each of the sub-atlas images (210, 220, 230, 240, 250); - performing a deformable registration using a registration method allowing non-rigid transformations wherein the patient image is registered with the sub-atlas image (210, 220, 230, 240, 250) of said selected atlas using said rigid registration result for the sub-atlas image of said selected atlas as initialization, said deformable registration resulting in a deformable registration result; - segmenting at least one region of interest (21, 22, 23, 24, 25) in the patient image at least partly based on said deformable registration result. - performing, for each of at least two atlases, each comprising one or more segmented regions of interest (21, 22, 23, 24, 25), a preparatory registration using a registration method allowing rigid transformations wherein the patient image is registered with a complete atlas image acquired from the atlas, resulting in a preparatory registration result for said complete atlas image which is used as initialization for at least one of the following rigid registration steps; - 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 sub-atlas image (210, 220, 230, 240, 250), respectively, said sub-atlas images being sub-sets of, and derived from, different complete atlas images comprising one or more segmented regions of interest (21, 22, 23, 24, 25), wherein each of said rigid registrations of the patient image with each of said sub-atlas images comprises multiple consecutive registrations where the size of the sub-atlas image is reduced before each subsequent registration, said rigid registrations resulting in a rigid registration result for each of the sub-atlas images; - determining a degree of similarity for each of the sub-atlas images (210, 220, 230, 240, 250) based on said rigid registration results; - selecting an atlas on basis of the determined degree of similarity for each of the sub-atlas images (210, 220, 230, 240, 250); - performing a deformable registration using a registration method allowing non-rigid transformations wherein the patient image is registered with the sub-atlas image (210, 220, 230, 240, 250) of said selected atlas using said rigid registration result for the sub-atlas image of said selected atlas as initialization, said deformable registration resulting in a deformable registration result; - segmenting at least one region of interest (21, 22, 23, 24, 25) in the patient image at least partly based on said deformable registration result.