To perform a more accurate and detailed diagnosis of a brain disease, a diagnosis server of the brain disease diagnosis system for diagnosing a brain disease of an examined person includes: an acquiring unit for acquiring a brain image of the examined person so as to obtain an acquired image a region setting unit for setting a plurality of regions in the acquired image an individual index value calculating unit for calculating an individual index value based on a pixel value of the acquired image, in each of the plurality of regions a whole index value calculating unit for calculating a whole index value by weighting the individual index value of each of the plurality of regions a diagnosis unit for diagnosing the brain disease of the examined person based on the whole index value and an output unit for outputting information indicating a diagnosis outcome.
