Multi-scale V-net architecture with deep feature CRF layers for brain extraction

Abstract Background Brain extraction is a computational necessity for researchers using brain imaging data. However, the complex structure of the interfaces between the brain, meninges and human skull have not allowed a highly robust solution to emerge. While previous methods have used machine learning with structural and geometric priors in mind, with the development of Deep Learning (DL), there has been an increase in Neural Network based methods. Most proposed DL models focus on improving the training data despite the clear gap between groups in the amount and quality of accessible training data between. Methods We propose an architecture we call Efficient V-net with Additional Conditional Random Field Layers (EVAC+). EVAC+ has 3 major characteristics: (1) a smart augmentation strategy that improves training efficiency, (2) a unique way of using a Conditional Random Fields Recurrent Layer that improves accuracy and (3) an additional loss function that fine-tunes the segmentation output. We compare our model to state-of-the-art non-DL and DL methods. Results Results show that even with limited training resources, EVAC+ outperforms in most cases, achieving a high and stable Dice Coefficient and Jaccard Index along with a desirable lower Surface (Hausdorff) Distance. More importantly, our approach accurately segmented clinical and pediatric data, despite the fact that the training dataset only contains healthy adults. Conclusions Ultimately, our model provides a reliable way of accurately reducing segmentation errors in complex multi-tissue interfacing areas of the brain. We expect our method, which is publicly available and open-source, to be beneficial to a wide range of researchers.