Hi Conor, the FB scan is just to get the patient into an approximate position prior to BH. We place the isocentre at the centre of the PTV on both scans, but both will have different coordinates based on the nature of the scans. Ideally, when the patient is set up in FB and enter BH all deltas will be in tolerance reproducing what happens at CT, but this is not usually the case and requires some adjustment for Lat and Long directions.
If as you say you have completely different isocentre locations, you could use the FB to initially position the patient, enter BH and make the adjustments and when the patients exhales capture a new reference for the FB setup which should be ‘below’ the BH setup going forward. Hope this helps.