1. An aligning apparatus comprising: a partial medical image storing means for storing a plurality of partial medical images, each obtained by imaging a predetermined region of a subject; a reference image storing means for storing an overall reference image representing a normal anatomy of the anatomical structures of the entire subject; a first aligning means for aligning an anatomical structure in the imaged region of each of the plurality of partial medical images with the corresponding anatomical structure in the overall reference image; and a second aligning means for aligning two partial medical images of the plurality of partial medical images having an overlapping area in the imaged region such that an anatomical structure in the overlapping area of one of the two partial medical images is aligned with the corresponding anatomical structure in the overlapping area of the other of the two partial medical images after: the anatomical structure in the overlapping area of one of the two partial medical images is aligned with the corresponding anatomical structure in the overall reference image by the first aligning means; and the anatomical structure in the overlapping area of the other of the two partial medical images is aligned with the corresponding anatomical structure in the overall reference image by the first aligning means.