The invention discloses an image processing apparatus, an image processing system, and an image processing method. The image processing apparatus according an exemplary embodiment of the present invention estimates for a plurality of positions in a target image an estimated value of an error in registration for acquiring a third three-dimensional image by deforming at least one of a first three-dimensional image of a subject and a second three-dimensional image, one of the three-dimensional images being the target image, designates a cross section in the target image, acquires a statistical value of the error in the designated cross section based on the estimated value estimated for a plurality of positions in the cross section, and displays the statistical value.