Generating, with respect to each of the three-dimensional image and the three-dimensional comparison image, a plurality of tomographic images orthogonal to a central axis of each vertebra of the subject along the central axis, calculating a first characteristic amount representing a profile in a direction orthogonal to the central axis at each point on the central axis based on the tomographic images, calculating a second characteristic amount representing a profile in a direction of the central axis at each point on the central axis based on the tomographic images, calculating a third characteristic amount representing regularity of disposition of each vertebra at each point on the central axis based on the calculated first and second characteristic amounts, and aligning positions of the third characteristic amount calculated from the three-dimensional image and the third characteristic amount calculated from the three-dimensional comparison image along the central axis.