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In post-operative radiotherapy for prostate cancer, the cancerous prostate gland has been surgically removed, so the clinical target volume (CTV) to be irradiated encompasses the microscopic spread of tumor cells, which cannot be visualized in typical clinical images such as computed tomography or magnetic resonance imaging. In current clinical practice, physicians segment CTVs manually based on their relationship with nearby organs and other clinical information, per clinical guidelines. Automating post-operative prostate CTV segmentation with traditional image segmentation methods has been a major challenge. Here, we propose a deep learning model to overcome this problem by segmenting nearby organs first, then using their relationship with the CTV to assist CTV segmentation. The model proposed is trained using labels clinically approved and used for patient treatment, which are subject to relatively large inter-physician variations due to the absence of a visual ground truth. The model achieves an average Dice similarity coefficient (DSC) of 0.87 on a holdout dataset of 50 patients, much better than established methods, such as atlas-based methods (DSC<0.7). The uncertainties associated with automatically segmented CTV contours are also estimated to help physicians inspect and revise the contours, especially in areas with large inter-physician variations. We also use a 4-point grading system to show that the clinical quality of the automatically segmented CTV contours is equal to that of approved clinical contours manually drawn by physicians.