1. A three-dimensional image processing apparatus comprising: a storage unit that stores data of a plurality of mask images and data of a plurality of contrast images, each of the plurality of mask images being obtained by radiographing a subject to be examined with radiation incident on the subject from different respective directions before contrast medium injection, each of the plurality of contrast images being obtained by radiographing the subject to be examined in respective different radiation incident directions after the contrast medium injection; a reconstruction unit that reconstructs first three-dimensional image data from the plurality of mask image data and reconstructs second three-dimensional image data from the plurality of contrast image data; a positional deviation correcting unit that corrects positional deviation of the first three-dimensional image with respect to the second three-dimensional image on the basis of the comparison result between an anatomical structure in a partial region of the first three-dimensional image data and an anatomical structure in a corresponding partial region of the second three-dimensional image data, and creates third three-dimensional image data, including an extraction unit which extracts the partial regions of the first and second three-dimensional image data using a threshold related to bone; and a processing unit that performs subtraction between the second three-dimensional image data and the third three-dimensional data and creates fourth three-dimensional image data.