A method and system for fully automatic segmentation the prostate in magnetic resonance (MR) image data is disclosed. Intensity normalization is performed on an MR image of a patient to adjust for global contrast changes between the MR image and other MR scans and to adjust for intensity variation within the MR image due to an endorectal coil used to acquire the MR image. An initial prostate segmentation in the MR image is obtained by aligning a learned statistical shape model of the prostate to the MR image using marginal space learning (MSL). The initial prostate segmentation is refined using one or more trained boundary classifiers.