Application of Automatic Segmentation on Super-Resolution Reconstruction MR Images of the Abnormal Fetal Brain

T. Deprest, L. Fidon, F. De Keyzer, M. Ebner, J. Deprest, P. Demaerel, L. De Catte, T. Vercauteren, S. Ourselin, S. Dymarkowski, M. Aertsen

Research output: Contribution to journalArticlepeer-review


BACKGROUND AND PURPOSE: Fetal brain MR imaging is clinically used to characterize fetal brain abnormalities. Recently, algorithms have been proposed to reconstruct high-resolution 3D fetal brain volumes from 2D slices. By means of these reconstructions, convolutional neural networks have been developed for automatic image segmentation to avoid labor-intensive manual annotations, usually trained on data of normal fetal brains. Herein, we tested the performance of an algorithm specifically developed for segmentation of abnormal fetal brains. MATERIALS AND METHODS: This was a single-center retrospective study on MR images of 16 fetuses with severe CNS anomalies (gestation, 21-39 weeks). T2-weighted 2D slices were converted to 3D volumes using a super-resolution reconstruction algorithm. The acquired volumetric data were then processed by a novel convolutional neural network to perform segmentations of white matter and the ventricular system and cerebellum. These were compared with manual segmentation using the Dice coefficient, Hausdorff distance (95th percentile), and volume difference. Using interquartile ranges, we identified outliers of these metrics and further analyzed them in detail. RESULTS: The mean Dice coefficient was 96.2%, 93.7%, and 94.7% for white matter and the ventricular system and cerebellum, respectively. The Hausdorff distance was 1.1, 2.3, and 1.6 mm, respectively. The volume difference was 1.6, 1.4, and 0.3 mL, respectively. Of the 126 measurements, there were 16 outliers among 5 fetuses, discussed on a case-by-case basis. CONCLUSIONS: Our novel segmentation algorithm obtained excellent results on MR images of fetuses with severe brain abnormalities. Analysis of the outliers shows the need to include pathologies underrepresented in the current data set. Quality control to prevent occasional errors is still needed.

Original languageEnglish
Pages (from-to)486-491
Number of pages6
JournalAJNR. American journal of neuroradiology
Issue number4
Publication statusPublished - 1 Apr 2023


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