1. A method for segmenting a plurality of target structures in three-dimensional image data comprising: (a) providing pre-segmented training images of structures representing the target structures; (b) modeling, using a computer, inter-structure structure ordered spatial dependency for each of the target structures from the pre-segmented training images by placing all pre-segmented training images in a common reference coordinate system using the known neighboring structures as reference anchor structures; (c) integrating the ordered spatial dependency with a segmentation algorithm by registering anchor structures from the three-dimensional image data to the reference anchor structures used in step (b); (d) determining an optimal sequence for segmentation of the plurality of target structures; and (e) sequentially segmenting each of the plurality of target structures according to the optimal sequence thus restricting the plausible segmentation space for each subsequent target structure in the sequence to produce enhanced segmentations of the target structures.