Brain extraction or whole brain segmentation is an important first step in many of the neuroimage analysis pipelines. The accuracy and robustness of brain extraction, therefore, is crucial for the accuracy of the entire brain analysis process. State-of-the-art brain extraction techniques rely heavily on the accuracy of alignment or registration between brain atlases and query brain anatomy, and/or make assumptions about the image geometry; therefore have limited success when these assumptions do not hold or image registration fails. With the aim of designing an accurate, learning-based, geometry-independent and registration-free brain extraction tool in this study, we present a technique based on an auto-context convolutional neural network (CNN), in which intrinsic local and global image features are learned through 2D patches of different window sizes. We consider two different architectures: 1) a voxelwise approach based on three parallel 2D convolutional pathways for three different directions (axial, coronal, and sagittal) that implicitly learn 3D image information without the need for computationally expensive 3D convolutions, and 2) a fully convolutional network based on the U-net architecture. Posterior probability maps generated by the networks are used iteratively as context information along with the original image patches to learn the local shape and connectedness of the brain to extract it from non-brain tissue.The brain extraction results we have obtained from our CNNs are superior to the recently reported results in the literature on two publicly available benchmark datasets, namely LPBA40 and OASIS, in which we obtained Dice overlap coefficients of 97.73% and 97.62%, respectively. Significant improvement was achieved via our auto-context algorithm. Furthermore, we evaluated the performance of our algorithm in the challenging problem of extracting arbitrarily-oriented fetal brains in reconstructed fetal brain magnetic resonance imaging (MRI) datasets. In this application our voxelwise auto-context CNN performed much better than the other methods (Dice coefficient: 95.97%), where the other methods performed poorly due to the non-standard orientation and geometry of the fetal brain in MRI. Through training, our method can provide accurate brain extraction in challenging applications. This in-turn may reduce the problems associated with image registration in segmentation tasks.
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