Generative adversarial network for segmentation of motion affected neonatal brain MRI

N. Khalili; E. Turk; M. Zreik; M. A. Viergever; M. J. N. L. Benders; I. Isgum

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arXiv · 1906.04704

Generative adversarial network for segmentation of motion affected neonatal brain MRI

N. Khalili·E. Turk·M. Zreik·M. A. Viergever·M. J. N. L. Benders·I. Isgum

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Abstract

Automatic neonatal brain tissue segmentation in preterm born infants is a prerequisite for evaluation of brain development. However, automatic segmentation is often hampered by motion artifacts caused by infant head movements during image acquisition. Methods have been developed to remove or minimize these artifacts during image reconstruction using frequency domain data. However, frequency domain data might not always be available. Hence, in this study we propose a method for removing motion artifacts from the already reconstructed MR scans. The method employs a generative adversarial network trained with a cycle consistency loss to transform slices affected by motion into slices without motion artifacts, and vice versa. In the experiments 40 T2-weighted coronal MR scans of preterm born infants imaged at 30 weeks postmenstrual age were used. All images contained slices affected by motion artifacts hampering automatic tissue segmentation. To evaluate whether correction allows more accurate image segmentation, the images were segmented into 8 tissue classes: cerebellum, myelinated white matter, basal ganglia and thalami, ventricular cerebrospinal fluid, white matter, brain stem, cortical gray matter, and extracerebral cerebrospinal fluid. Images corrected for motion and corresponding segmentations were qualitatively evaluated using 5-point Likert scale. Before the correction of motion artifacts, median image quality and quality of corresponding automatic segmentations were assigned grade 2 (poor) and 3 (moderate), respectively. After correction of motion artifacts, both improved to grades 3 and 4, respectively. The results indicate that correction of motion artifacts in the image space using the proposed approach allows accurate segmentation of brain tissue classes in slices affected by motion artifacts.

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N. Khalili, E. Turk, M. Zreik, M. A. Viergever, M. J. N. L. Benders, I. Isgum. 2019-06-11. Generative adversarial network for segmentation of motion affected neonatal brain MRI. https://arxiv.org/abs/1906.04704

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