A CT imaging system has a rotatable gantry, a table movable fore and aft through an opening defined within the rotatable gantry, and a controller that incrementally moves a subject disposed on the table through a number of discrete data acquisition positions for the acquisition of physiologically gated CT data. The controller also coordinates acquisition of imaging data from the subject at a first data acquisition position within a physiological cycle of the subject and only advances the subject to a next data acquisition position if the imaging data acquired at the first data acquisition position is deemed acceptable. The controller also detects irregularities and physiological motion of the subject and responsive thereto, suspends data acquisition until the irregularity passes, such as, suspending data acquisition until a next cardiac cycle if a heart arrhythmia is detected.