1. A medical image processing apparatus, comprising: a three-dimensional model estimating section that estimates a three-dimensional model of living tissue based on a two-dimensional image of an image of the living tissue inputted from a medical image pickup apparatus; a local region setting section that sets a plurality of local regions around a target pixel in the two-dimensional image; a shape feature value calculating section that uses three-dimensional coordinate data corresponding to each of the plurality of local regions and calculates shape feature values of respective voxels corresponding to the target pixel based on the three-dimensional model of the living tissue estimated by the three-dimensional model estimating section; a shape feature value selecting section that selects, as an optimum shape feature value of a voxel corresponding to the target pixel, a shape feature value calculated according to one local region including an optimum three-dimensional coordinate data amount among the plurality of shape feature values calculated according to the plurality of local regions; and an elevated shape detecting section that detects an elevated shape existing in the two-dimensional image based on a selection result of the shape feature value selecting section.