1. An image position aligning apparatus, comprising: band image generating means, for generating a plurality of first band images and a plurality of second band images that represent structures of different frequency bands within a first and a second image of a same portion of a single subject; positional shift amount obtaining means, for obtaining amounts of positional shift among corresponding positions within the first band images and the second band images of corresponding frequency bands; aligning means, for separately deforming pairs of the first band images and the second band images of corresponding frequency bands based on the amounts of positional shift; and reconstructing means, for sequentially reconstructing at least one of the deformed first band images and second band images from low frequency bands, and for obtaining at least one of the first image and the second image in a deformed state.