A medical imaging system having at least one medical imaging device providing image data of a subject is provided. The medical imaging system further includes a processing system programmed to train a deep learning (DL) network using a plurality of training images to predict noise in input data. The plurality of training images includes a plurality of excitation (NEX) images acquired for each line of k-space training data. The processing system is further programmed to use the trained DL network to determine noise in the image data of the subject and to generate a denoised medical image of the subject having reduced noise based on the determined noise in the image data.