Context-endcoding for neural network based skull stripping in magnetic resonance imaging

Skull stripping is usually the first step for most brain analysisprocess in magnetic resonance images. A lot of deep learn-ing neural network based methods have been developed toachieve higher accuracy. Since the 3D deep learning modelssuffer from high computational cost and are subject to GPUmemory limit challenge, a variety of 2D deep learning meth-ods have been developed. However, existing 2D deep learn-ing methods are not equipped to effectively capture 3D se-mantic information that is needed to achieve higher accuracy.In this paper, we propose a context-encoding method to em-power the 2D network to capture the 3D context information.For the context-encoding method, firstly we encode the 2Dfeatures of original 2D network, secondly we encode the sub-volume of 3D MRI images, finally we fuse the encoded 2Dfeatures and 3D features with semantic encoding classifica-tion loss. To get computational efficiency, although we en-code the sub-volume of 3D MRI images instead of buildinga 3D neural network, extensive experiments on three bench-mark Datasets demonstrate our method can achieve superioraccuracy to state-of-the-art alternative methods with the dicescore 99.6% on NFBS and 99.09 % on LPBA40 and 99.17 %on OASIS.