1. A medical image processing apparatus comprising: a three-dimensional model estimating unit for estimating a three-dimensional model of a living tissue based on a two-dimensional image of an image of the living tissue in a body cavity, the two-dimensional image inputted from a medical image pickup apparatus; a detection target area setting unit for setting a detection target area of a lesion with elevated shape in the three-dimensional model; a shape feature value calculating unit for calculating shape feature values indicative of a state of the shape at each data point included in the detection target area; a three-dimensional shape detecting unit for detecting a lesion area with locally elevated shape existing in the detection target area based on a threshold process with respect to the shape feature values; and a threshold determining unit for determining thresholds applied in the three-dimensional shape detecting unit, wherein the threshold determining unit determines the thresholds applied in the three-dimensional shape detecting unit based on coordinates in an axial direction perpendicular to the two-dimensional image of the detection target area.