1. A method, comprising: a first step of receiving a first image of a prostate in a planning phase, wherein the first image is acquired with a first imaging modality and is semi-automatically segmented, and wherein a binary mask and contours of the prostate are saved; a second step of acquiring a second image of the prostate, wherein the second image is acquired with a second imaging modality; a third step of performing an alignment to compensate for orientation misalignments between the first image and the second image, wherein the alignment uses user specified point correspondences on the prostate in the first and second images to compute rough translations and when three or more point correspondences are specified, a rigid registration estimate and an initial guess for the amount of anatomic deformations is computed automatically; a fourth step of performing a manual adjustment of the alignment to account for translational misalignments between the first and second images by dragging slices from the first image to match content of the second image; a fifth step of acquiring third images of the prostate, wherein the third images are acquired with the second imaging modality and are compounded into a three-dimensional (3D) image; a sixth step of using an initial registration between the first and second images resulting from the alignment and the binary mask from the planning phase to segment the prostate in the compounded 3D image; a seventh step of performing a second registration and then a third registration different from the second registration on distance maps generated from boundaries of the segmentations of the prostate in the first and second images; an eighth step of transforming the first image along with its included annotations and segmentation structures onto the third images to produce a fourth image; a ninth step of displaying the fourth image with a region of interest mapped thereon; and monitoring quality of alignment of the region of interest in the displayed fourth image, and re-running the second step and the fifth through eighth steps if the quality deteriorates due to patient immobilization or anatomic shifts, or re-running the second through eighth steps if the quality deteriorates for large misalignments.