DDCSR: A Novel End-to-End Deep Learning Framework for Cortical Surface Reconstruction from Diffusion MRI

Abstract: Diffusion MRI (dMRI) plays a crucial role in studying brain white matter connectivity. Cortical surface reconstruction (CSR), including the inner whiter matter (WM) and outer pial surfaces, is one of the key tasks in dMRI analyses such as fiber tractography and multimodal MRI analysis. Existing CSR methods rely on anatomical T1-weighted data and map them into the dMRI space through inter-modality registration. However, due to the low resolution and image distortions of dMRI data, inter-modality registration faces significant challenges. This work proposes a novel end-to-end learning framework, DDCSR, which for the first time enables CSR directly from dMRI data. DDCSR consists of two major components, including: (1) an implicit learning module to predict a voxel-wise intermediate surface representation, and (2) an explicit learning module to predict the 3D mesh surfaces. Compared to several baseline and advanced CSR methods, we show that the proposed DDCSR can largely increase both accuracy and efficiency. Furthermore, we demonstrate a high generalization ability of DDCSR to data from different sources, despite the differences in dMRI acquisitions and populations.