Multi-level Glioma Segmentation using 3D U-Net Combined Attention Mechanism with Atrous Convolution

Accurate segmentation of glioma from 3D medical images is vital to numerous clinical endpoints. While manual segmentation is subjective and time-consuming, fully automated extraction is quite imperative and challenging due to the intrinsic heterogeneity of tumor structures. In this study, we propose a multi-level glioma segmentation framework, 3D Residual-Attention-Atrous U-Net (RAAU-Net), using 3D U-Net combined attention mechanism with atrous convolution. The 3D RAAU-Net can extract contextual information by combining low- and high-resolution feature maps. The attention mechanism is embedded in each skip connection layer of 3D RAAU-Net to enhance feature representations. Meanwhile, the atrous convolution is adopted in the whole network architecture to incorporate large and rich semantic information. Furthermore, we design a new training scheme to reduce false positives and enhance generalization. Eventually, our proposed segmentation method is evaluated on the validation dataset from the Multimodal Brain Tumor Image Segmentation Challenge (BraTS) 2018 and achieve a competitive result with average Dice score of 88% for the whole tumor, 79% for the tumor core and 73% for the enhancing tumor, respectively. Quantitative results and visual analysis have proven that these improvements in 3D RAAU-Net are effective and achieve a better segmentation accuracy compared with the baseline.