The embodiments described herein relate to a protocol controller for a medical diagnostic imaging system. In one embodiment, two or more distinct study protocols are active on a medical diagnostic imaging system at the same time. In another embodiment, control of a medical diagnostic imaging system is changed at each stage of a study protocol sequence to optimize study performance. In yet another embodiment, a protocol is created from a collection of macros that control a medical diagnostic imaging system. Other embodiments are provided, and each of the embodiments described herein can be used alone or in combination with one another.