The invention provides for a magnetic resonance imaging system (100) for acquiring magnetic resonance data (142 148 158) with a pulse sequence (140) for multiple slice acquisition performed over multiple repetition cycles. The magnetic resonance imaging system further comprises a processor (540) for controlling the magnetic resonance imaging system. The execution of the instructions cause the processor to: acquire (200) a first slice group (142) of the magnetic resonance data during a first repetition cycle extract (202) first central k space data (144) from the first slice group reconstruct (204) first navigator data (146) using the first central k space data. Execution of the instructions causes the processor to repeatedly: acquire (206) a subsequent slice group (148) of the magnetic resonance data during a subsequent repetition cycle extract (208) subsequent central k space data (150) from the subsequent slice group reconstruct (210) subsequent navigator data (152) using the subsequent central k space data determining (212) a mapping (154) from the first navigator data to the subsequent navigator data and correct (214) the acquisition of a next slice group of the magnetic resonance data using the mapping.
