Bone segmentation on whole-body CT using convolutional neural network with novel data augmentation techniques. (June 2020)

• Record Type: Journal Article
• Authors: Noguchi, Shunjiro; Nishio, Mizuho; Yakami, Masahiro; Nakagomi, Keita; Togashi, Kaori
• Is Part Of: Computers in biology and medicine. Volume 121(2020)
• Publication Date: 2020-06
• Subjects: Bone -- Segmentation -- CT -- CNN -- U-net -- Data augmentation -- Mixup -- RICAP; Medicine -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; 610.285
• DOI: 10.1016/j.compbiomed.2020.103767
• Languages: English
• ISSNs: 0010-4825

Abstract

Abstract: Background: The purpose of this study was to develop and evaluate an algorithm for bone segmentation on whole-body CT using a convolutional neural network (CNN). Methods: Bone segmentation was performed using a network based on U-Net architecture. To evaluate its performance and robustness, we prepared three different datasets: (1) an in-house dataset comprising 16, 218 slices of CT images from 32 scans in 16 patients; (2) a secondary dataset comprising 12, 529 slices of CT images from 20 scans in 20 patients, which were collected from The Cancer Imaging Archive; and (3) a publicly available labelled dataset comprising 270 slices of CT images from 27 scans in 20 patients. To improve the network's performance and robustness, we evaluated the efficacy of three types of data augmentation technique: conventional method, mixup, and random image cropping and patching (RICAP). Results: The network trained on the in-house dataset achieved a mean Dice coefficient of 0.983 ± 0.005 on cross validation with the in-house dataset, and 0.943 ± 0.007 with the secondary dataset. The network trained on the public dataset achieved a mean Dice coefficient of 0.947 ± 0.013 on 10 randomly generated 15-3-9 splits of the public dataset. These results outperform those reported previously. Regarding augmentation technique, the conventional method, RICAP, and a combination of these were effective. Conclusions: The CNN-based model achieved accurate bone segmentation on whole-body CT, with generalizability to various scan conditions. Data augmentation techniques enabled construction of an accurate and robust model even with a small dataset. Highlights: CNN-based model was developed for bone segmentation on whole-body CT. Markedly high segmentation accuracy was achieved on in-house dataset. Its robustness was validated by testing on a secondary dataset obtained under different scan conditions. Data augmentation techniques enabled construction of an accurate model even with a small dataset.