Robust semi-automatic segmentation method: an expert assistant tool for muscles in CT and MR data

Image muscle segmentation is useful to quantitatively assess musculoskeletal diseases by extracting biomarkers such as shape, texture and water diffusivity metrics. Although volumetric manual segmentation is time consuming and a bottleneck in practice, fully automatic approaches are still in progress to reach an acceptable accuracy. In this paper, we provide a robust semi-automated tool to segment two musculoskeletal systems, i.e. thigh and shoulder in MRI and CT modalities, respectively. The tool only needs a few manually labelled cross-sections to build a directed graph-structure of corresponding points between the successive spaced slices. The boundaries of each muscle are obtained by performing a spline interpolation based on the directed graph-structure. Each muscle label and its corresponding 3D mesh are deduced using post-processing techniques. We evaluated the tool on 26 MRI thighs and 16 CT shoulders. Three metrics along with inter-muscle overlapping were employed to evaluate the tool by comparison to an expert manual segmentation and a publicly available tools (ITK-SNAP, 3D Slicer). The results showed a mean Dice $0.988 \pm 0.003$0.988 +/- 0.003, and Hausdorff Distance $4.86 \pm 1.67$4.86 +/- 1.67 mm in comparison to the manual reference for thigh muscle segmentation, and a mean Dice $0.961 \pm 0.005$0.961 +/- 0.005 and Hausdorff Distance $2.42 \pm 0.79$2.42 +/- 0.79 mm for shoulder muscle segmentation, outperformed the other methods. The tool is proposed as slicer module available at https://github.com/latimagine/SlicerSpline.