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 the object which is obtained by picking up an inside of the object; 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 of the plurality of regions and a frequency component of the one region; and a lesion detection reference setting section for performing a threshold determination for determining whether data included in a three-dimensional model which corresponds to the one region is sparse or dense with respect to each of the feature value according to the grayscale and the frequency component, and further setting a lesion detection reference which is used when detecting a locally protruding lesion in the three-dimensional model which corresponds to the one region based on a result of the threshold determination.