Methods and systems are provided for automated graphical prescriptions with deep learning systems. In one embodiment, a method for a medical imaging system comprises acquiring, by the medical imaging system, localizer images of a subject, generating, by a trained neural network system, a graphical prescription using the localizer images, and performing, by the medical imaging system, a scan of the subject according to the graphical prescription. In this way, a desired region of interest of the subject may be accurately scanned with minimal input from an operator of the medical imaging system.