1. An image registration device, comprising: a rigid registration unit configured to perform a rigid registration of a first input image with a second input image, which is a reference, to obtain first deformation information; a first non-rigid registration unit configured to perform a first non-rigid registration of the first input image with the second input image by taking the first deformation information as the initial deformation information to obtain second deformation information; and a second non-rigid registration unit configured to perform a second non-rigid registration of the first input image with the second input image by taking the second deformation information as the initial deformation information to obtain third deformation information.