1. A magnetic field distortion calculation device, comprising: image acquisition unit for acquiring first and second three-dimensional images with different imaging timings that are acquired by imaging a target part of a subject using an MRI apparatus; region extraction unit for extracting first and second shape-invariant regions corresponding to each other from the first and second three-dimensional images; first registration unit for acquiring a first deformation vector of each point on the first shape-invariant region with respect to each corresponding point on the second shape-invariant region by performing rigid registration between the first and second shape-invariant regions; second registration unit for acquiring a second deformation vector of each point on the first shape-invariant region of the first three-dimensional image with respect to each corresponding point on the second shape-invariant region of the second three-dimensional image by performing non-rigid registration between the first and second three-dimensional images in the first and second shape-invariant regions; and magnetic field distortion vector calculation unit for calculating a magnetic field distortion vector, which represents relative magnetic field distortion between the first and second three-dimensional images, at each point on the first three-dimensional image based on the first and second deformation vectors.