Robust Bayesian brain extraction by integrating structural subspace-based spatial prior into deep neural networks

Accurate and robust brain extraction, or skull stripping, is essential for studying brain development, aging, and neurological disorders. However, brain images exhibit substantial data heterogeneity due to differences in contrast and geometric characteristics across various diseases, medical institutions and age groups. A fundamental challenge lies in effectively capturing the high-dimensional spatial-intensity distributions of the brain. This paper introduces a novel Bayesian brain extraction method that integrates a structural subspace-based prior, represented as a mixture-of-eigenmodes, with deep learning-based classification to achieve accurate and robust brain extraction. Specifically, we used structural subspace model to effectively capture global spatial-structural distributions of the normal brain. Leveraging this global spatial prior, a multi-resolution, position-dependent neural network is employed to effectively model the local spatial-intensity distributions. A patch-based fusion network is then used to combine these global and local spatial-intensity distributions for final brain extraction. The proposed method has been rigorously evaluated using multi-institutional datasets, including healthy scans across lifespan, images with lesions, and images affected by noise and artifacts, demonstrating superior segmentation accuracy and robustness over the state-of-the-art methods. Our proposed method holds promise for enhancing brain extraction in practical clinical applications.