Cardiac MRI Segmentation With a Dilated CNN Incorporating Domain-Specific Constraints

Abstract

Semantic segmentation of cardiac MR images is a challenging task due to its importance in medical assessment of heart diseases. Having a detailed localization of specific regions of interest such as Right and Left Ventricular Cavities and Myocardium, doctors can infer important information about the presence of cardiovascular diseases, which are today a major cause of death globally. This paper addresses the problem of semantic segmentation in cardiac MR images using a dilated Convolutional Neural Network. Opting for dilated convolutions allowed us to work in full resolution throughout the network's layers, preserving localization accuracy, while maintaining a relatively small number of trainable parameters. To assist the network's training process we designed a custom loss function. Furthermore, we developed new augmentation techniques and also adapted existing ones, to cope for the lack of sufficient training images. Consequently, the training set increases not only by amount, but by substance as well, and the network trains quickly and efficiently without overfitting. Our pre- and post-processing steps are also crucial to the whole process. We apply our methodology for the Right and Left Ventricles (RV, LV) and also the Myocardium (MYO) according to the Automated Cardiac Diagnosis Challenge (ACDC) with promising results. Submitting our algorithm's predictions to the Post-2017-MICCAI-challenge testing phase, we achieved similar scores (average Dice coefficient 0.916) on the test data set compared to the state of the art featured in the ACDC leaderboard, but with significantly fewer parameters than the leading method. Our approach outperforms other methods featuring dilated convolutions in this challenge up until now.