1. A medical image processing apparatus, comprising: a three-dimensional model estimating section for estimating a three-dimensional model of an object based on a two-dimensional image of an image of the object which is inputted from a medical image pickup apparatus; an image dividing section for dividing the two-dimensional image into a plurality of regions each of which includes at least one or more pixels; a feature value calculation section for calculating a feature value according to a grayscale of each pixel in one region for each of the plurality of regions; and a lesion detection reference setting section for setting a lesion detection reference for detecting a locally protruding lesion in the regions of the three-dimensional model which correspond to each of the plurality of regions, based on the feature value according to the grayscale.