Brain MR images segmentation using 3D CNN with features recalibration mechanism for segmented CT generation

The segmentation of MR (magnetic resonance) images is a simple approach to create Pseudo CT images which are useful for many medical imaging analysis applications. One of the main challenges of this pro-cess is the bone segmentation of brain MR images. Deep convolutional neural networks (CNNs) have been widely and efficiently applied to perform MR images segmentation. The aim of this work is to propose a novel excitation-based CNN by recalibrating the network features adaptively to enhance the bone seg-mentation by segmenting the brain MR images into three tissue classes: bone, soft tissue, and air. The proposed method combines two types of features excitation mechanisms namely: (1) spatial squeeze and channel excitation block (cSE) and (2) channel squeeze and spatial excitation block (sSE). The two blocks are combined sequentially and integrated seamlessly into a 3D convolutional encoder decoder network. The novelty of this work emerges in the combination of the two excitation blocks sequentially to improve the segmentation performance and reduce the model complexity. The proposed approach is evaluated through a comparison with computed tomography (CT) images as ground truth and validated with other methods in the literature that applied deep CNN approaches to perform MR image segmenta-tion for PET attenuation correction. Brain MR and CT datasets which consist of 50 patients are used to evaluate the proposed method. The segmentation performance of the three brain classes is evaluated using precision, recall, dice similarity coefficient (DSC), and Jaccard index. The presented method improves the bone tissue segmentation compared to the baseline model and other methods in the liter-ature where the DSC is improved from 0.6278 +/- 0.0006 to 0.6437 +/- 0.0006 with an improvement per-centage of 2.53% for bone class. The proposed excitation-based segmentation network architecture demonstrates promising and competitive results compared with other methods in the literature and reduces the model complexity thanks to the sequential combination of the two excitation blocks. (c) 2022 Elsevier B.V. All rights reserved.