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arXiv · 2006.06432

Fully-automated deep learning slice-based muscle estimation from CT images for sarcopenia assessment

Fahdi Kanavati·Shah Islam·Zohaib Arain·Eric O. Aboagye·Andrea Rockall
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Abstract

Objective: To demonstrate the effectiveness of using a deep learning-based approach for a fully automated slice-based measurement of muscle mass for assessing sarcopenia on CT scans of the abdomen without any case exclusion criteria. Materials and Methods: This retrospective study was conducted using a collection of public and privately available CT images (n = 1070). The method consisted of two stages: slice detection from a CT volume and single-slice CT segmentation. Both stages used Fully Convolutional Neural Networks (FCNN) and were based on a UNet-like architecture. Input data consisted of CT volumes with a variety of fields of view. The output consisted of a segmented muscle mass on a CT slice at the level of L3 vertebra. The muscle mass is segmented into erector spinae, psoas, and rectus abdominus muscle groups. The output was tested against manual ground-truth segmentation by an expert annotator. Results: 3-fold cross validation was used to evaluate the proposed method. The slice detection cross validation error was 1.41+-5.02 (in slices). The segmentation cross validation Dice overlaps were 0.97+-0.02, 0.95+-0.04, 0.94+-0.04 for erector spinae, psoas, and rectus abdominus, respectively, and 0.96+-0.02 for the combined muscle mass. Conclusion: A deep learning approach to detect CT slices and segment muscle mass to perform slice-based analysis of sarcopenia is an effective and promising approach. The use of FCNN to accurately and efficiently detect a slice in CT volumes with a variety of fields of view, occlusions, and slice thicknesses was demonstrated.

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Fahdi Kanavati, Shah Islam, Zohaib Arain, Eric O. Aboagye, Andrea Rockall. 2020-06-10. Fully-automated deep learning slice-based muscle estimation from CT images for sarcopenia assessment. https://arxiv.org/abs/2006.06432

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