In this paper, a method is developed that reconstructs a high resolution image from an arbitrary set of multi-slice 3D MR images with a high in-plane resolution and a low through-plane resolution. Such images are often recorded to increase the efficiency of the acquisition. With a model of the acquisition of MR images, which is improved compared to previous super-resolution methods for MR images, a large system with linear equations is obtained. With the conjugated gradient method and this linear system, a high resolution image is reconstructed from MR images of an object. Also, a new and efficient method to apply an affine transformation to multi-dimensional images is presented. This method is used to efficiently reconstruction the high resolution image from multislice MR images with arbitrary orientations of the slices.