Multi-atlas based neonatal brain extraction using a two-level patch-based label fusion strategy

Compared to adults, brain extraction from magnetic resonance (MR) images of newborn infants is particularly challenging due to their smaller brain size, which causes lower spatial resolution, lower tissue contrast and ambiguous tissue intensity distribution. In this work, a multi-atlas patch-based label fusion method is presented for automatic brain extraction from neonatal head MR images. In this method, a number of atlases are first selected uniformly among a set of training images. After nonlinear alignment of the selected atlas images to the target image, a probabilistic gray level-coded brain mask is created and used to assign brain/non-brain labels to voxels with different degree of uncertainty using a modified non-local patch-based label fusion method based on the integration of low-level and in-depth search patch selection strategies. Experiments with 40 neonates aged between 37 and 44 weeks showed an average Dice, Jaccard and Conformity coefficients of 0.993, 0.986 and 0.986, respectively. We compared the performance of the proposed method with two multi atlas-based methods, i.e. NLPB and MASS, and two popular non-learning-based methods, i.e. BSE and BET. Compared to these methods, our method achieved higher accuracy with brain masks very close to manually extracted ones and produced lower false negative and false positive rates. Our proposed method allows for accurate and efficient brain extraction, a crucial step in brain MRI applications such as brain tissue segmentation and volume estimation in neonates. (C) 2019 Elsevier Ltd. All rights reserved.