Cascaded Triplanar Autoencoder M-Net for Fully Automatic Segmentation of Left Ventricle Myocardial Scar From Three-Dimensional Late Gadolinium-Enhanced MR Images

While three-dimensional (3D) late gadolinium-enhanced (LGE) magnetic resonance (MR) imaging provides good conspicuity of small myocardial lesions with short acquisition time, it poses a challenge for image analysis as a large number of axial images are required to be segmented. We developed a fully automatic convolutional neural network (CNN) called cascaded triplanar autoencoder M-Net (CTAEM-Net) to segment myocardial scar from 3D LGE MRI. Two sub-networks were cascaded to segment the left ventricle (LV) myocardium and then the scar within the pre-segmented LV myocardium. Each sub-network contains three autoencoder M-Nets (AEM-Nets) segmenting the axial, sagittal and coronal slices of the 3D LGE MR image, with the final segmentation determined by voting. The AEM-Net integrates three features: (1) multi-scale inputs, (2) deep supervision and (3) multi-tasking. The multi-scale inputs allow consideration of the global and local features in segmentation. Deep supervision provides direct supervision to deeper layers and facilitates CNN convergence. Multi-task learning reduces segmentation overfitting by acquiring additional information from autoencoder reconstruction, a task closely related to segmentation. The framework provides an accuracy of 86.43% and 90.18% for LV myocardium and scar segmentation, respectively, which are the highest among existing methods to our knowledge. The time required for CTAEM-Net to segment LV myocardium and the scar was 49.72 $\pm$ 9.69s and 120.25 $\pm$ 23.18s per MR volume, respectively. The accuracy and efficiency afforded by CTAEM-Net will make possible future large population studies. The generalizability of the framework was also demonstrated by its competitive performance in two publicly available datasets of different imaging modalities.