A magnetic resonance (MR) system (10) and method (100) maintains geometric alignment of diagnostic scans during an examination of a patient (12). At least one processor (40) is programmed to, in response to repositioning of the patient (12) during the examination, perform an updated survey scan of the patient (12). A scan completed during the examination is selected as a template scan. A transformation map between the template scan and the updated survey scan is determined using a registration algorithm, and the transformation map is applied to a scan geometry of a remaining diagnostic scan of the examination. A scan plan for the remaining diagnostic scan is generated using the updated scan geometry. The remaining diagnostic scan is performed according to the scan plan.
