Essential parameters needed for a U-Net-based segmentation of individual bones on planning CT images in the head and neck region using limited datasets for radiotherapy application

Objective. The field of radiotherapy is highly marked by the lack of datasets even with the availability of public datasets. Our study uses a very limited dataset to provide insights on essential parameters needed to automatically and accurately segment individual bones on planning CT images of head and neck cancer patients. Approach. The study was conducted using 30 planning CT images of real patients acquired from 5 different cohorts. 15 cases from 4 cohorts were randomly selected as training and validation datasets while the remaining were used as test datasets. Four experimental sets were formulated to explore parameters such as background patch reduction, class-dependent augmentation and incorporation of a weight map on the loss function. Main results. Our best experimental scenario resulted in a mean Dice score of 0.93 +/- 0.06 for other bones (skull, mandible, scapulae, clavicles, humeri and hyoid), 0.93 +/- 0.02 for ribs and 0.88 +/- 0.03 for vertebrae on 7 test cases from the same cohorts as the training datasets. We compared our proposed solution approach to a retrained nnU-Net and obtained comparable results for vertebral bones while outperforming in the correct identification of the left and right instances of ribs, scapulae, humeri and clavicles. Furthermore, we evaluated the generalization capability of our proposed model on a new cohort and the mean Dice score yielded 0.96 +/- 0.10 for other bones, 0.95 +/- 0.07 for ribs and 0.81 +/- 0.19 for vertebrae on 8 test cases. Significance. With these insights, we are challenging the utilization of an automatic and accurate bone segmentation tool into the clinical routine of radiotherapy despite the limited training datasets.