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; wherein the overall reference image has average densities and positions of anatomical structures, obtained by imaging multitude of subjects; and wherein: each of the plurality of partial medical images is a tomographic image obtained by tomography; the overall reference image is a gray image in which anatomical structures obtained from multitudes of tomographic images obtained by tomography are represented in normal densities; the overall reference image represents the entirety of a human body; and the first aligning means performs positional alignment of the partial medical images with corresponding portions of the overall reference image, based on data regarding imaged portions attached to the partial medical images, wherein the overall reference image has recorded therein a plurality of feature points of a human body; and the first aligning means detects feature points in the partial medical images based on data regarding the imaged portions attached thereto, and employs the feature points within the overall reference image corresponding to the detected feature points to perform positional alignment, and wherein the feature points represent positional information of distinctive points to represent anatomical structure of the overall image.