Concern 1: I think we need to do intrafractional imaging in addition to AlignRT to be sure that the target is in its correct location. Can we in addition to AlignRT use for example triggered imaging to see the markers in the liver and online/offline control/evaluate the marker position (The Use of Triggered Imaging for Intrafraction Target Verification in Liver SBRT Breathhold, Walb 2019)? Internal diaphragm is reported to correlate better with liver than the bony structures in the CBCT (Availability of applying diaphragm matching with the breath-holding technique in stereotactic body radiation therapy for liver tumors Daisuke Kawahara et al, 2016). Which one is better for external ROI with AlignRT: bony chest wall or diaphragm to correlate with the liver movement/location during the treatment? VisionRT suggests in reference guide to include bony chest wall for liver SBRT, as you mentioned. I think we need more data and papers of correlations of the ROIs to the liver/markers before we can say which ROI is better and can we overall rely on AlignRT alone during the beam delivery, if we are treating the internal moving target.
Concern 2: I share your concern. There is always a risk of posture changes concerning the BH and chest wall posture, once the patient travels several centimeters in BH from CBCT_ISO to treatment_ISO and at the end of that trip we acquire VRT surface for treatment. At least patients needs to be well trained what will happen. I agree with Daniel that succeeding of the surface used for the treatment and additionally in this case succeeding of the couch shift action after CBCT and thereby target accuracy should be verified somehow before treatment. 1) kV/kV images? for approximate verification: 2) use separate AlignRT fields for setup and treatment. Ask patient to BH to treatment VRT (just acquired based on CBCT), pause, change field and monitor setup BH surface for a while to see are the RTDs that much out of the zero values as you shifted the couch based on CBCT match and let patient breathe again. Go back to treatment VRT. 3) Once you monitor patient in FB at BH field, deltas should be different from BH all the time as much IF the patient can relax her/his ROI area back to original setup position after all the BHs (which they do not exactly usually do) but these 2 and 3 are only for approximate evaluation that the BH amplitude remains the same all the time.
Hope there was something useful