A Novel Mis-Seg-Focus Loss Function Based on a Two-Stage nnU-Net Framework for Accurate Brain Tissue Segmentation

Brain tissue segmentation plays a critical role in the diagnosis, treatment, and study of brain diseases. Accurately identifying these boundaries is essential for improving segmentation accuracy. However, distinguishing boundaries between different brain tissues can be challenging, as they often overlap. Existing deep learning methods primarily calculate the overall segmentation results without adequately addressing local regions, leading to error propagation and mis-segmentation along boundaries. In this study, we propose a novel mis-segmentation-focused loss function based on a two-stage nnU-Net framework. Our approach aims to enhance the model’s ability to handle ambiguous boundaries and overlapping anatomical structures, thereby achieving more accurate brain tissue segmentation results. Specifically, the first stage targets the identification of mis-segmentation regions using a global loss function, while the second stage involves defining a mis-segmentation loss function to adaptively adjust the model, thus improving its capability to handle ambiguous boundaries and overlapping anatomical structures. Experimental evaluations on two datasets demonstrate that our proposed method outperforms existing approaches both quantitatively and qualitatively.