DDSurfer: A Weakly‐Supervised Dual‐Stream Deep Learning Framework for Cortical Surface Reconstruction From Diffusion MRI

Cortical surface reconstruction of white matter and pial surfaces from diffusion MRI (dMRI) is critical for neuroimaging analyses, including tractography, connectomics, and multimodal data integration. However, obtaining these surfaces from dMRI data is inherently challenged by its low spatial resolution and poor tissue contrast. Currently, this relies on T1-weighted images, from which the surfaces are reconstructed and then registered to the dMRI space-a process affected by inaccurate inter-modality registration. This study introduces DDSurfer, an end-to-end deep learning framework that directly generates high-fidelity cortical surfaces from dMRI data. DDSurfer leverages a novel dual-stream architecture that processes and synergistically fuses complementary microstructural features from dMRI, learning a diffeomorphic transformation for subject-specific surface reconstruction. The model is trained using a robust weakly-supervised strategy with automatically generated pseudo-ground-truth surfaces. Extensive evaluations on diverse datasets demonstrate that DDSurfer surpasses traditional methods in geometric accuracy, morphological consistency, and generalization. By providing a computationally efficient and robust T1-weighted-independent solution, DDSurfer overcomes a major bottleneck in dMRI, delivering a practical tool to advance accurate dMRI-centric connectomics and surface-based investigations. Source code and implementation as an interactive 3D Slicer module are publicly available at: https://github.com/ChengjinLii/DDSurfer.