Automatic multiple sclerosis lesion segmentation in the spinal cord using 3 T and 7 T MP2RAGE images

To develop a deep learning-based fully automated framework for segmenting multiple sclerosis (MS) lesions in the spinal cord (SC) using images derived from MP2RAGE acquisitions.

This retrospective multicenter study included 472 MRI volumes from 422 subjects (mean age 52±12.5 years), comprising 402 patients with MS and 20 healthy controls, acquired at three centers using 3 T and 7 T MRI systems. MP2RAGE-UNI images were preprocessed and analyzed using the Spinal Cord Toolbox (SCT). The multicenter 3 T dataset was divided into training (60%), validation (20%), and testing (20%) subsets, while the 7 T dataset was reserved for testing. The proposed method (UNIseg), based on the nnU-Net v2 architecture, was trained on the multicenter dataset and compared with the current benchmark (seg_ms_lesion_mp2rage, available in SCT v6.3 and earlier versions), which was trained on single-center MP2RAGE-UNI data. Segmentation performance was evaluated using Dice coefficient and lesion-wise metrics by comparing both UNIseg and the benchmark against reference standard. Statistical comparisons were performed using the Wilcoxon signed-rank test.

On the 3 T dataset, UNIseg achieved a mean Dice score of 0.67, significantly outperforming the benchmark (p ≤ 0.01). Lesion-wise sensitivity and precision were 0.81 and 0.92, respectively, with fewer false-positive segmentations. On the 7 T dataset, UNIseg also demonstrated significantly higher performance (p ≤ 0.001), although segmentation performance was lower than that observed at 3 T CONCLUSION: UNIseg provides a robust and efficient approach for segmentation of lesions, improving accuracy compared with existing methods, especially for 3 T data. The trained model and code are publicly available in SCT v6.4 and later.