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Organ motion and set-up uncertainties limit optimization of 3D treatment planning by expanding the width of PTV margins required to ensure target coverage. Transabdominal ultrasound-based stereotactic guidance is a safe and direct method for correcting patient positioning. Our experience with the BAT system in a large cohort of prostate cancer patients revealed that substantial daily isocenter corrections were encountered in a large percentage of cases. This data would suggest that daily clinical isocenter misalignments are greater than would be expected from published data on organ motion and set-up variations encountered in the study setting.