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To address the lack of accurate dose estimation method in cone beam computed tomography (CBCT), we performed point dose metal oxide semiconductor field-effect transistor (MOSFET) measurements and Monte Carlo (MC) simulations. A Varian On-Board Imager® (OBI) was employed to measure point doses in the polymethyl methacrylate (PMMA) CT phantoms with MOSFETs for standard and low dose modes. A MC model of the OBI x-ray tube was developed using BEAMnrc/EGSnrc MC system and validated by the half value layer, x-ray spectrum and lateral and depth dose profiles. We compared the weighted computed tomography dose index (CTDIw) between MOSFET measurements and MC simulations. The CTDIw was found to be 8.39 cGy for the head scan and 4.58 cGy for the body scan from the MOSFET measurements in standard dose mode, and 1.89 cGy for the head and 1.11 cGy for the body in low dose mode, respectively. The CTDIw from MC compared well to the MOSFET measurements within 5% differences. In conclusion, a MC model for Varian CBCT has been established and this approach may be easily extended from the CBCT geometry to multi-detector CT geometry.