1. A medical image processing apparatus comprising: an emphasizing processing unit which performs processing to emphasize a specific structure among structures composing a subject on each of a first image and a second image obtained by capturing the same subject at different points in time; a positioning unit which matches a position of the specific structure in the first image and the second image based on the first image and the second image with the specific structure emphasized; and a difference image generating unit which generates a difference image between the first image without emphasizing processing and the second image without emphasizing processing with the position of the specific structure matched, wherein, the first image and the second image are thoracic portion X-ray images and the specific structure is a back rib bone, and wherein the emphasizing processing unit performs filtering processing which emphasizes an edge of a vertical component on the first image and the second image, and emphasizes the back rib bone by adding an image on which the filtering processing is performed and an original image.