For a multi-modal emission tomography system, an improved control system increases the likelihood of optimal image quality, satisfaction of physician goals, and/or avoids repetition in scanning and the corresponding increase in dose burden. The control system is divided into two or more arrangements. One arrangement receives goal information and outputs reconstruction settings and generic scan settings to satisfy the goal information. Another arrangement converts the generic scan settings to emission tomography system-specific scan settings, which are used to detect emissions. The separation of the arrangements allows independent operation so that different system-specific conversions may be used for different systems. Another possible arrangement performs a quality check on the detected emissions, allowing feedback for altering the system-specific scan settings to possibly avoid scan repetition and/or allowing feedforward for reconstruction to optimize the reconstruction settings based on the acquired data to be reconstructed.
