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The nnU-Net based method for automatic segmenting fetal brain tissues

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Abstract

The magnetic resonance (MR) images of fetuses make it possible for doctors to detect out pathological fetal brains in early stages. Brain tissue segmentation is prerequisite for making brain morphology and volume analyses. nnU-Net is an automatic segmentation method based on deep learning. It can adaptively configure itself, so as to adapt to a specific task via preprocessing, network architecture, training, and post-processing. Therefore, we adapt nnU-Net to segment seven types of fetal brain tissues, including external cerebrospinal fluid, gray matter, white matter, ventricle, cerebellum, deep gray matter, and brainstem. With regard to the characteristics of the FeTA 2021 data, some adjustments are made to the original nnU-Net, so that it can segment seven types of fetal brain tissues precisely as far as possible. The average segmentation results on FeTA 2021 training data demonstrate that our advanced nnU-Net is superior to the peers including SegNet, CoTr, AC U-Net and ResUnet. Its average segmentation results are 0.842, 11.759 and 0.957 in terms of Dice, HD95 and VS criteria. Moreover, the experimental results on FeTA 2021 test data further demonstrate that our advanced nnU-Net has obtained good segmentation performance of 0.774, 14.699 and 0.875 in terms of Dice, HD95 and VS, ranked the third in FeTA 2021 challenge. Our advanced nnU-Net realized the task for segmenting the fetal brain tissues using MR images of different gestational ages, which can help doctors to make correct and seasonable diagnoses.

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Acknowledgements

This work is supported in part by the National Natural Science Foundation of China under Grant Nos. of 62076159, 12031010, and 61673251; and is also supported by the Fundamental Research Funds for the Central Universities under Grant Nos. of GK202105003 and 202207017. We acknowledge those who organized the FeTA 2021 challenge and published the training data and the related informations for us to use in this research.

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  1. Ying Peng, Yandi Xu, and Mingzhao Wang have contributed equally to this work.

Authors and Affiliations

  1. School of Computer Science, Shaanxi Normal University, West Chang’an Avenue, Chang’an District, Xi’an, 710119, Shaanxi, People’s Republic of China

    Ying Peng, Mingzhao Wang, Huiquan Zhang & Juanying Xie

  2. School of Medicine, Tulane University, 1430 Tulane Ave, New Orleans, LA, 70112, USA

    Yandi Xu

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  1. Ying Peng
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Correspondence to Juanying Xie.

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Peng, Y., Xu, Y., Wang, M. et al. The nnU-Net based method for automatic segmenting fetal brain tissues. Health Inf Sci Syst 11, 17 (2023). https://doi.org/10.1007/s13755-023-00220-3

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