Automated Muscle Segmentation from Clinical CT Using Bayesian U Net for Personalized Musculoskeletal Modeling
We propose a method for automatic segmentation of individual muscles from a clinical CT. The method uses Bayesian convolutional neural networks with the U Net architecture, using Monte Carlo dropout that infers an uncertainty metric in addition to the segmentation label. We evaluated the performance of the proposed method using two data sets: 20 fully annotated CTs of the hip and thigh regions and 18 partially annotated CTs that are publicly available from The Cancer Imaging Archive (TCIA) database. The experiments showed a Dice coefficient (DC) of 0.891+ 0.016 (mean+ std) and an average symmetric surface distance (ASD) of 0.994+ 0.230 mm over 19 muscles in the set of 20 CTs. These results were statistically significant improvements compared to the state of the art hierarchical multi atlas method which resulted in 0.845 0.031 DC and 1.556 0.444 mm ASD. We evaluated validity of the uncertainty metric in the multi class organ segmentation problem and demonstrated a correlation between the pixels with high uncertainty and the segmentation failure. One application of the uncertainty metric in active learning is demonstrated, and the proposed query pixel selection method considerably reduced the manual annotation cost for expanding the training data set. The proposed method allows an accurate patient specific analysis of individual muscle shapes in a clinical routine. This would open up various applications including personalization of biomechanical simulation and quantitative evaluation of muscle atrophy.
IEEE Transactions on Medical Imaging