Optimized automated cardiac MR scar quantification with GAN-based data augmentation

Background: The clinical utility of late gadolinium enhancement (LGE) cardiac MRI is limited by the lack of standardization, and time-consuming postprocessing. In this work, we tested the hypothesis that a cas-caded deep learning pipeline trained with augmentation by synthetically generated data would improve model accuracy and robustness for automated scar quantification.Methods: A cascaded pipeline consisting of three consecutive neural networks is proposed, starting with a bounding box regression network to identify a region of interest around the left ventricular (LV) my-ocardium. Two further nnU-Net models are then used to segment the myocardium and, if present, scar. The models were trained on the data from the EMIDEC challenge, supplemented with an extensive syn-thetic dataset generated with a conditional GAN. Results: The cascaded pipeline significantly outperformed a single nnU-Net directly segmenting both the myocardium (mean Dice similarity coefficient (DSC) (standard deviation (SD)): 0.84 (0.09) vs 0.63 (0.20), p < 0.01) and scar (DSC: 0.72 (0.34) vs 0.46 (0.39), p < 0.01) on a per-slice level. The inclusion of the syn-thetic data as data augmentation during training improved the scar segmentation DSC by 0.06 ( p < 0.01). The mean DSC per-subject on the challenge test set, for the cascaded pipeline augmented by synthetic generated data, was 0.86 (0.03) and 0.67 (0.29) for myocardium and scar, respectively.Conclusion: A cascaded deep learning-based pipeline trained with augmentation by synthetically gen-erated data leads to myocardium and scar segmentations that are similar to the manual operator, and outperforms direct segmentation without the synthetic images.(c) 2022 The Author(s). Published by Elsevier B.V.This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )

Automated summary

In this study, a cascaded deep learning pipeline trained with augmentation by synthetically generated data was proposed to improve the accuracy and robustness of scar quantification in late gadolinium enhancement cardiac MRI. The results showed that the cascaded pipeline outperformed direct segmentation methods and the augmentation with synthetic data enhanced the accuracy of scar segmentation.