One or more blood vessel regions that represent one or more blood vessels that govern the function of an organ are extracted from a three dimensional anatomical image that represents the three dimensional shape of the organ. Next, blood vessel governed regions, the functions of which are governed by a single blood vessel, are estimated, based on each blood vessel region, while regions other than the blood vessel governed regions are estimated to be non governed regions. Index values to be indices of diagnosis are calculated by analyzing evaluation values that constitute a three dimensional functional image, without using the evaluation values included in the non governed regions. Then, the calculated index values are output to a display screen or the like.