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Background: To evaluate a novel CBCT conversion algorithm for dose calculation implemented in a research version of a treatment planning system (TPS). Methods: The algorithm was implemented in a research version of RayStation (v. 11B-DTK, RaySearch, Stockholm, Sweden). CBCTs acquired for each ten head and neck (HN), gynecology (GYN) and lung cancer (LNG) patients were collected and converted using the new algorithm (CBCTc). A bulk density overriding technique implemented in the same version of the TPS was used for comparison (CBCTb). A deformed CT (dCT) was created by using deformable image registration of the planning CT (pCT) to the CBCT to reduce anatomical changes. All treatment plans were recalculated on the pCT, dCT, CBCTc and the CBCTb. The resulting dose distributions were analyzed using the MICE toolkit (NONPIMedical AB Sweden, Umeå) with local gamma analysis, with 1% dose difference and 1 mm distance to agreement criteria. A Wilcoxon paired rank sum test was applied to test the differences in gamma pass rates (GPRs). A p value smaller than 0.05 considered statistically significant. Results: The GPRs for the CBCTb method were systematically lower compared to the CBCTc method. Using the 10% dose threshold and the dCT as reference the median GPRs were for the CBCTc method were 100% and 99.8% for the HN and GYN cases, respectively. Compared to that the GPRs of the CBCTb method were lower with values of 99.8% and 98.0%, for the HN and GYN cases, respectively. The GPRs of the LNG cases were 99.9% and 97.5% for the CBCTc and CBCTb method, respectively. These differences were statistically significant. The main differences between the dose calculated on the CBCTs and the pCTs were found in regions near air/tissue interfaces, which are also subject to anatomical variations. Conclusion: The dose distribution calculated using the new CBCTc method showed excellent agreement with the dose calculated using dCT and pCT and was superior to the CBCTb method. The main reasons for deviations of the calculated dose distribution were caused by anatomical variations between the pCT and the corrected CBCT. [ABSTRACT FROM AUTHOR]