A deep learning system for automated, multi-modality 2D segmentation of vertebral bodies and intervertebral discs

Fractures in vertebral bodies are among the most common complications of osteoporosis and other bone diseases. However, studies that aim to predict future fractures and assess general spine health must manually delineate vertebral bodies and intervertebral discs in imaging studies for further radiomic analysis. This study aims to develop a deep learning system that can automatically and rapidly segment (delineate) vertebrae and discs in MR, CT, and X-ray imaging studies.

We constructed a neural network to output 2D segmentations for MR, CT, and X-ray imaging studies. We trained the network on 4490 MR, 550 CT, and 1935 X-ray imaging studies (post-data augmentation) spanning a wide variety of patient populations, bone disease statuses, and ages from 2005 to 2020. Evaluated using 5-fold cross validation, the network was able to produce median Dice scores > 0.95 across all modalities for vertebral bodies and intervertebral discs (on the most central slice for MR/CT and on image for X-ray). Furthermore, radiomic features (skewness, kurtosis, mean of positive value pixels, and entropy) calculated from predicted segmentation masks were highly accurate (r ≥ 0.96 across all radiomic features when compared to ground truth). Mean time to produce outputs was <1.7 s across all modalities.

Our network was able to rapidly produce segmentations for vertebral bodies and intervertebral discs for MR, CT, and X-ray imaging studies. Furthermore, radiomic quantities derived from these segmentations were highly accurate. Since this network produced outputs rapidly for these modalities which are commonly used, it can be put to immediate use for radiomic and clinical imaging studies assessing spine health.