EVC-Net: Multi-scale V-Net with Conditional Random Fields for Brain Extraction

Brain extraction is one of the first steps of pre-processing 3D brain MRI data. It is a prerequisite for any forthcoming brain imaging analyses. However, it is not a simple segmentation problem due to the complex structure of the brain and human head. Although multiple solutions have been proposed in the literature, we are still far from having truly robust methods. While previous methods have used machine learning with structural/geometric priors, with the development of deep learning in computer vision tasks, there has been an increase in proposed convolutional neural network architectures for this semantic segmentation task. Yet, most models focus on improving the training data and loss functions with little change in the architecture. In this paper, we propose a novel architecture we call EVC-Net. EVC-Net adds lower scale inputs on each encoder block. This enhances the multi-scale scheme of the V-Net architecture, hence increasing the efficiency of the model. Conditional Random Fields, a popular approach for image segmentation before the deep learning era, are re-introduced here as an additional step for refining the network's output to capture fine-grained results in segmentation. We compare our model to state-of-the-art methods such as HD-BET, Synthstrip and brainy. Results show that even with limited training resources, EVC-Net achieves higher Dice Coefficient and Jaccard Index along with lower surface distance.