AtlasSeg: Atlas prior guided dual-U-Net for tissue segmentation in fetal brain MRI

Accurate automatic tissue segmentation in fetal brain MRI is a crucial step in clinical diagnosis but remains challenging, particularly due to the dynamically changing anatomy and tissue contrast during fetal development. Existing segmentation networks can only implicitly learn age-related features, leading to a decline in accuracy at extreme gestational ages (GAs). To improve segmentation performance throughout gestation, we introduce AtlasSeg, a dual-U-shape convolution network that explicitly integrates GA-specific information as guidance. By providing a publicly available fetal brain atlas with segmentation labels corresponding to relevant GAs, AtlasSeg effectively extracts age-specific patterns in the atlas branch and generates precise tissue segmentation in the segmentation branch. Multi-scale spatial attention feature fusions are constructed during both encoding and decoding stages to enhance feature flow and facilitate better information interactions between two branches. We compared AtlasSeg with ten well-established networks with a seven-tissue segmentation task in our in-house and two public datasets, achieving the highest average Dice similarity coefficient. The improvement was particularly evident in extreme early or late GA cases, where training data was scare. Furthermore, AtlasSeg exhibited minimal performance degradation on low-quality images with contrast changes and noise, attributed to its anatomical shape priors. Overall, AtlasSeg demonstrated enhanced segmentation accuracy, better consistency across fetal ages, and robustness to perturbations, making it a powerful tool for reliable fetal brain MRI tissue segmentation, particularly suited for diagnostic assessments during early gestation.