Dosimetric evaluation of synthetic CT for head and neck radiotherapy generated by a patch-based three-dimensional convolutional neural network

Purpose To develop and evaluate a patch-based convolutional neural network (CNN) to generate synthetic computed tomography (sCT) images for magnetic resonance (MR)-only workflow for radiotherapy of head and neck tumors. A patch-based deep learning method was chosen to improve robustness to abnormal anatomies caused by large tumors, surgical excisions, or dental artifacts. In this study, we evaluate whether the generated sCT images enable accurate MR-based dose calculations in the head and neck region. Methods We conducted a retrospective study on 34 patients with head and neck cancer who underwent both CT and MR imaging for radiotherapy treatment planning. To generate the sCTs, a large field-of-view T2-weighted Turbo Spin Echo MR sequence was used from the clinical protocol for multiple types of head and neck tumors. To align images as well as possible on a voxel-wise level, CT scans were nonrigidly registered to the MR (CTreg). The CNN was based on a U-net architecture and consisted of 14 layers with 3 x 3 x 3 filters. Patches of 48 x 48 x 48 were randomly extracted and fed into the training. sCTs were created for all patients using threefold cross validation. For each patient, the clinical CT-based treatment plan was recalculated on sCT using Monaco TPS (Elekta). We evaluated mean absolute error (MAE) and mean error (ME) within the body contours and dice scores in air and bone mask. Also, dose differences and gamma pass rates between CT- and sCT-based plans inside the body contours were calculated. Results sCT generation took 4 min per patient. The MAE over the patient population of the sCT within the intersection of body contours was 75 +/- 9 Hounsfield Units (HU) (+/- 1 SD), and the ME was 9 +/- 11 HU. Dice scores of the air and bone masks (CTreg vs sCT) were 0.79 +/- 0.08 and 0.70 +/- 0.07, respectively. Dosimetric analysis showed mean deviations of -0.03% +/- 0.05% for dose within the body contours and -0.07% +/- 0.22% inside the >90% dose volume. Dental artifacts obscuring the CT could be circumvented in the sCT by the CNN-based approach in combination with Turbo Spin Echo (TSE) magnetic resonance imaging (MRI) sequence that typically is less prone to susceptibility artifacts. Conclusions The presented CNN generated sCTs from conventional MR images without adding scan time to the acquisition. Dosimetric evaluation suggests that dose calculations performed on the sCTs are accurate, and can therefore be used for MR-only radiotherapy treatment planning of the head and neck.