  Automatic fetal brain tissue segmentation can enhance the quantitative
assessment of brain development at this critical stage. Deep learning methods
represent the state of the art in medical image segmentation and have also
achieved impressive results in brain segmentation. However, effective training
of a deep learning model to perform this task requires a large number of
training images to represent the rapid development of the transient fetal brain
structures. On the other hand, manual multi-label segmentation of a large
number of 3D images is prohibitive. To address this challenge, we segmented 272
training images, covering 19-39 gestational weeks, using an automatic
multi-atlas segmentation strategy based on deformable registration and
probabilistic atlas fusion, and manually corrected large errors in those
segmentations. Since this process generated a large training dataset with noisy
segmentations, we developed a novel label smoothing procedure and a loss
function to train a deep learning model with smoothed noisy segmentations. Our
proposed methods properly account for the uncertainty in tissue boundaries. We
evaluated our method on 23 manually-segmented test images of a separate set of
fetuses. Results show that our method achieves an average Dice similarity
coefficient of 0.893 and 0.916 for the transient structures of younger and
older fetuses, respectively. Our method generated results that were
significantly more accurate than several state-of-the-art methods including
nnU-Net that achieved the closest results to our method. Our trained model can
serve as a valuable tool to enhance the accuracy and reproducibility of fetal
brain analysis in MRI.
