Towards contrast-agnostic soft segmentation of the spinal cord

Spinal cord segmentation is clinically relevant and is notably used to compute spinal cord cross-sectional area (CSA) for the diagnosis and monitoring of cord compression or neurodegenerative diseases such as multiple sclerosis. While several semi and automatic methods exist, one key limitation remains: the segmentation depends on the MRI contrast, resulting in different CSA across contrasts. This is partly due to the varying appearance of the boundary between the spinal cord and the cerebrospinal fluid that depends on the sequence and acquisition parameters. This contrast-sensitive CSA adds variability in multi-center studies where protocols can vary, reducing the sensitivity to detect subtle atrophies. Moreover, existing methods enhance the CSA variability by training one model per contrast, while also producing binary masks that do not account for partial volume effects. In this work, we present a deep learning-based method that produces soft segmentations of the spinal cord that are stable across MRI contrasts. Using the Spine Generic Public Database of healthy participants (n=267; contrasts=6), we first generated participant-wise soft ground truth (GT) by averaging the binary segmentations across all 6 contrasts. These soft GT, along with aggressive data augmentation and a regression-based loss function, were then used to train a U-Net model for spinal cord segmentation. We evaluated our model against state-of-the-art methods and performed ablation studies involving different GT mask types, loss functions, contrast-specific models and domain generalization methods. Our results show that using the soft average segmentations along with a regression loss function reduces CSA variability (p<0.05, Wilcoxon signed-rank test). The proposed spinal cord segmentation model generalizes better than the state-of-the-art contrast-specific methods amongst unseen datasets, vendors, contrasts, and pathologies (compression, lesions), while accounting for partial volume effects. Our model is integrated into the Spinal Cord Toolbox (v6.2 and higher).