A system and method for using learned discriminative models to segment a border of an anatomical structure in a three dimensional (3D) image is disclosed. A discriminative probability model is computed for each voxel in the 3D image. Thresholding is performed on each discriminative probability model. One or more two dimensional (2D) slices of the thresholded 3D image along X-Y planes are obtained. Seed regions are selected in the 2D slices. Morphological region growing is performed on the selected seed regions. An initial 3D segmentation is obtained. Boundary evolution is performed on the initial 3D segmentation. The segmented anatomical structure is removed. in the original 3D image.