Automated segmentation of head CT scans for computer-assisted craniomaxillofacial surgery applying a hierarchical patch-based stack of convolutional neural networks

Purpose Computer-assisted techniques play an important role in craniomaxillofacial surgery. As segmentation of three-dimensional medical imaging represents a cornerstone for these procedures, the present study was aiming at investigating a deep learning approach for automated segmentation of head CT scans. Methods The deep learning approach of this study was based on the patchwork toolbox, using a multiscale stack of 3D convolutional neural networks. The images were split into nested patches using a fixed 3D matrix size with decreasing physical size in a pyramid format of four scale depths. Manual segmentation of 18 craniomaxillofacial structures was performed in 20 CT scans, of which 15 were used for the training of the deep learning network and five were used for validation of the results of automated segmentation. Segmentation accuracy was evaluated by Dice similarity coefficient (DSC), surface DSC, 95% Hausdorff distance (95HD) and average symmetric surface distance (ASSD). Results Mean for DSC was 0.81 +/- 0.13 (range: 0.61 [mental foramen] - 0.98 [mandible]). Mean Surface DSC was 0.94 +/- 0.06 (range: 0.87 [mental foramen] - 0.99 [mandible]), with values > 0.9 for all structures but the mental foramen. Mean 95HD was 1.93 +/- 2.05 mm (range: 1.00 [mandible] - 4.12 mm [maxillary sinus]) and for ASSD, a mean of 0.42 +/- 0.44 mm (range: 0.09 [mandible] - 1.19 mm [mental foramen]) was found, with values < 1 mm for all structures but the mental foramen. Conclusion In this study, high accuracy of automated segmentation of a variety of craniomaxillofacial structures could be demonstrated, suggesting this approach to be suitable for the incorporation into a computer-assisted craniomaxillofacial surgery workflow. The small amount of training data required and the flexibility of an open source-based network architecture enable a broad variety of clinical and research applications.