St-RegSeg: an unsupervised registration-based framework for multimodal magnetic resonance imaging stroke lesion segmentation

Background: Stroke is one of the leading causes of disability and death worldwide. Ischemic stroke accounts for 75-90% of all stroke incidents. Assessing the size and location of the stroke lesion is crucial for treatment decisions, especially those related to urgent vascular reconstruction surgery. Magnetic resonance imaging (MRI) offers excellent soft tissue contrast and multimodal imaging characteristics, which can reflect changes in the physiological functions of brain soft tissues in patients with ischemic stroke. However, using deep learning (DL) techniques for MRI segmentation of stroke lesions still faces many challenges. On the one hand, single-modal segmentation models cannot effectively integrate multimodal information; on the other hand, there is a semantic content drift between multimodal stroke MRI images, leading to lower accuracy in subsequent multimodal image segmentation. To address these issues, we aimed to propose the stroke unsupervised registration and segmentation (St-RegSeg) framework.

Methods: The St-RegSeg framework integrates an unsupervised registration model, ConvNXMorph, and a segmentation model, nnUNet-v2, enabling both registration and segmentation of multimodal MRI images. The St-RegSeg framework was evaluated on the ISLES'22 dataset from three centers.

Results: The St-RegSeg framework demonstrated significant improvements in performance metrics and computational efficiency. Compared to advanced normalization tools (ANTs) [symmetric normalization (SyN)] + nnUNet-v2, the St-RegSeg framework improved the Dice similarity coefficient (DSC) by 25.31% in the registration phase, reduced mean squared error (MSE) by 17.36%, increased normalized cross-correlation (NCC) by 16.06%, and enhanced mutual information (MI) by 17.09%. Additionally, in the segmentation phase, it increased the DSC by 0.84%, and the overall inference speed was increased by 40.91 times. Compared to the suboptimal TransMorph + nnUNet-v2, the St-RegSeg framework improved the DSC by 3.68% in the registration phase, reduced MSE by 8.91%, increased NCC by 8.49%, enhanced MI by 6.18%, and in the segmentation phase, it raised the DSC by 0.5%, with the overall inference speed increased by 2.13 times.

Conclusions: The St-RegSeg framework provides a highly effective solution for the registration and segmentation of multimodal MRI images in ischemic stroke cases. Its performance metrics and computational efficiency significantly outperform existing methods, making it a promising tool for clinical applications. The code is open-sourced and available at: https://github.com/Cooper-Gu/St-RegSeg.