nnSegNeXt: A 3D Convolutional Network for Brain Tissue Segmentation Based on Quality Evaluation

Abstract

Accurate and automated segmentation of brain tissue images can significantly streamline clinical diagnosis and analysis. Manual delineation needs improvement due to its laborious and repetitive nature, while automated techniques encounter challenges stemming from disparities in magnetic resonance imaging (MRI) acquisition equipment and accurate labeling. Existing software packages, such as FSL and FreeSurfer, do not fully replace ground truth segmentation, highlighting the need for an efficient segmentation tool. To better capture the essence of cerebral tissue, we introduce nnSegNeXt, an innovative segmentation architecture built upon the foundations of quality assessment. This pioneering framework effectively addresses the challenges posed by missing and inaccurate annotations. To enhance the model’s discriminative capacity, we integrate a 3D convolutional attention mechanism instead of conventional convolutional blocks, enabling simultaneous encoding of contextual information through the incorporation of multiscale convolutional features. Our methodology was evaluated on four multi-site T1-weighted MRI datasets from diverse sources, magnetic field strengths, scanning parameters, temporal instances, and neuropsychiatric conditions. Empirical evaluations on the HCP, SALD, and IXI datasets reveal that nnSegNeXt surpasses the esteemed nnUNet, achieving Dice coefficients of 0.992, 0.987, and 0.989, respectively, and demonstrating superior generalizability across four distinct projects with Dice coefficients ranging from 0.967 to 0.983. Additionally, extensive ablation studies have been implemented to corroborate the effectiveness of the proposed model. These findings represent a notable advancement in brain tissue analysis, suggesting that nnSegNeXt holds the promise to significantly refine clinical workflows.

Keywords

• deep learning
• medical image analysis
• brain tissue segmentation
• convolutional attention mechanism
• data quality evaluation