In a medical image processing apparatus, a medical image processing method, and a medical image processing program, in a case where there are a plurality of past brain images, it is possible to select a past brain image with which the atrophy rate of the brain can be accurately calculated. An image acquisition unit acquires a target brain image Bt as a diagnostic target and a plurality of past brain images Bpi, which have earlier imaging dates and times than the target brain image Bt, for the same subject. A similarity calculation unit calculates the similarity between each of the plurality of past brain images Bpi and a standard brain image Bs. A selection unit selects a reference brain image B0 serving as a reference for calculating the amount of change of the brain from the plurality of past brain images Bpi.