Destruction for reperfusion in medical diagnostic ultrasound is synchronized to motion. Perfusion data for a volume is acquired sequentially for different segments of the volume. For a given segment, such as a planar region, motion tracking within the segment is performed. If sufficient registration or correlation exists at the completion of a sequence of scans for the current segment, then a lesser amount of movement is occurring. At this point, the transmission of contrast agent destructive acoustic energy is performed in the next segment. Tracking is repeated for the next segment to synchronize the switch to yet another segment. Other regions for tracking can be used. By controlling transmission of destruction pulses, more reliable perfusion quantities in a volume may be determined.