In a medical image processing apparatus, a medical image processing method, and a medical image processing program, the amount of change between two brain images having different imaging dates and times for the same patient is accurately acquired. A division unit 22 divides a brain included in a first brain image into a plurality of regions by performing registration between the first brain image including a brain of a subject and a standard brain image divided into a plurality of regions. A registration unit 23 performs registration between the first brain image and a second brain image that includes the brain of the subject and has a different imaging date and time from the first brain image. A change amount acquisition unit 24 acquires the amount of change from a corresponding region in the brain included in the first brain image, for at least one region of the plurality of regions in the brain included in the second brain image, based on the registration result.
