a segmentation method and system for medical images of a structure , including at least one substructure are described herein . examples of such structure and substructures are a vertebra and its spinal canal or a sacrum with its two foramens . the method consists of first providing a plurality of digital images representing consecutive slices of the structure . the set of images is then divided into groups for which initial substructures center position are estimated . using this information , the pixels corresponding to each substructure and common to all the images in the group are determined . iterations are performed between these two last steps until the best candidates are obtained . the method consists then in estimating the substructures center position in each image of the group . after the substructures have been identified in each image , the images are then processed to remove noise in the substructures , in the rest of the structure and outside the structure .