Methods and systems are provided for selectively denoising medical images. In an exemplary method, one or more deep learning networks are trained to map corrupted images onto a first type and a second type of artifacts present in corresponding corrupted images. Then the one or more trained learning networks are used to single out the first and second types of artifacts from a particular medical image. The first type of artifacts is removed to a first extent and the second type of artifacts is removed to a second extent. The first and second extents may be different. For example, one type of artifacts can be fully suppressed while the other can be partially removed form the medical image.