Automated Brain Tumour Segmentation Using Deep Fully Residual Convolutional Neural Networks

Automated brain tumour segmentation has the potential of making a massive improvement in disease diagnosis, surgery, monitoring and surveillance. However, this task is extremely challenging. Here, we describe our automated segmentation method using 2D CNNs that are based on U-Net. To deal with class imbalance effectively, we have used a weighted Dice loss function. We found that increasing the depth of the 'U' shape beyond a certain level results in a decrease in performance, so it is essential to choose an optimum depth. We also found that 3D contextual information cannot be captured by a single 2D network that is trained with patches extracted from multiple views whereas an ensemble of three 2D networks trained in multiple views can effectively capture the information and deliver much better performance. We obtained Dice scores of 0.79 for enhancing tumour, 0.90 for whole tumour, and 0.82 for tumour core on the BraTS 2018 validation set. Our method using 2D network consumes very less time and memory, and is much simpler and easier to implement compared to the state-of-the-art methods that used 3D networks; still, it manages to achieve comparable performance to those methods.