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.
We present a novel probabilistic shape representation that implicitly includes prior anatomical volume and adjacency information, termed the generalized log-ratio (GLR) representation. We demonstrate the usefulness of this representation in the task of thigh muscle segmentation. Analysis of the shapes and sizes of thigh muscles can lead to a better understanding of the effects of chronic obstructive pulmonary disease (COPD), which often results in skelet al muscle weakness in lower limbs. However, segmenting these muscles from one another is difficult due to a lack of distinctive features and inter-muscular boundaries that are difficult to detect. We overcome these difficulties by building a shape model in the space of GLR representations. We remove pose variability from the model by employing a presegmentation-based alignment scheme. We also design a rotationally invariant random forest boundary detector that learns common appearances of the interface between muscles from training data. We combine the shape model and the boundary detector into a fully automatic globally optimal segmentation technique. Our segmentation technique produces a probabilistic segmentation that can be used to generate uncertainty information, which can be used to aid subsequent analysis. Our experiments on challenging 3D magnetic resonance imaging data sets show that the use of the GLR representation improves the segmentation accuracy, and yields an average Dice similarity coefficient of @math , comparable to other state-of-the-art thigh segmentation techniques. Purpose Patient-specific quantitative assessments of muscle mass and biomechanical musculoskelet al simulations require segmentation of the muscles from medical images. The objective of this work is to automate muscle segmentation from CT data of the hip and thigh.