1. A magnetic field distortion calculation device, comprising: a processor configured for acquiring first and second three-dimensional images with different imaging timings that are acquired by imaging a target part of a subject performing with an MRI apparatus; extracting first and second shape-invariant regions corresponding to each other from the first and second three-dimensional images; 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; 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; calculating a fourth deformation vector of each point of the target part, which is included in the first three-dimensional image, with respect to each corresponding point of the target part included in the second three-dimensional image by removing magnetic field distortion included in the first three-dimensional image based on the magnetic field distortion vector and performing non-rigid registration between the first three-dimensional image from which the magnetic field distortion has been removed and the second three-dimensional image; and 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.