A method for automatic segmentation of intra-cochlear anatomy of a patient. The patient has an implanted ear and a normal contralateral ear. At least one computed tomography (CT) image is obtained to generate a first image corresponding to the normal contralateral ear and a second image corresponding to the implanted ear. Intra-cochlear surfaces of at least one first structure of interest (SOI) of the normal contralateral ear in the first image are segmented using at least one active shape model (ASM). Next, the segmented intra-cochlear surfaces in the first image is projected to the second image using a transformation function, thereby obtaining projected segmented intra-cochlear surfaces for the implanted ear in the second image.