Robust Segmentation of Lung Proton and Hyperpolarized Gas MRI with Vision Transformers and CNNs: A Comparative...

Accurate segmentation in medical imaging is essential for disease diagnosis and monitoring, particularly in lung imaging using proton and hyperpolarized gas MRI. However, image degradation due to noise and artifacts-especially in hyperpolarized gas MRI, where scans are acquired during breath-holds-poses challenges for conventional segmentation algorithms. This study evaluates the robustness of deep learning segmentation models under varying Gaussian noise levels, comparing traditional convolutional neural networks (CNNs) with modern Vision Transformer (ViT)-based models. Using a dataset of proton and hyperpolarized gas MRI slices from 56 participants, we trained and tested Feature Pyramid Network (FPN) and U-Net architectures with both CNN (VGG16, VGG19, ResNet152) and ViT (MiT-B0, B3, B5) backbones. Results showed that ViT-based models, particularly those using the SegFormer backbone, consistently outperformed CNN-based counterparts across all metrics and noise levels. The performance gap was especially pronounced in high-noise conditions, where transformer models retained higher Dice scores and lower boundary errors. These findings highlight the potential of ViT-based architectures for deployment in clinically realistic, low-SNR environments such as hyperpolarized gas MRI, where segmentation reliability is critical.