The present disclosure describes a computer-implemented method of transforming a low-resolution MR image to a high-resolution MR image using a deep CNN-based MRI SR network and a computer-implemented method of transforming an MR image to a pseudo-CT (sCT) image using a deep CNN-based sCT network. The present disclosure further describes a MR image-guided radiation treatment system that includes a computing device to implement the MRI SR and CT networks and to produce a radiation plan based in the resulting high resolution MR images and sCT images.