1. An image processing apparatus, comprising: an image input portion for receiving a base image and a reference image; a first window setting portion for setting a first window on one of said base image and said reference image; a second window setting portion for setting a second window on the other of base image and said reference image; an extraction portion for extracting at least one image feature value from the image in said first window; a modification portion for modifying said first window in at least one of a size and a shape thereof based on extracted said image feature value and modifying said second window in a size or a shape thereof in accordance with medication to said first window; and an operation portion for performing an operation to specify correspondence between the image in the modified first window and the image in the modified second window.