SimCortex v2: Joint Cortical Surface Reconstruction with Near-Zero Collisions and Self-Intersections

Abstract

Reconstructing cortical WM and pial surfaces from structural magnetic resonance imaging (MRI) is a prerequisite for surface-based neuroanatomical analysis, yet remains challenging because the cortex is thin and tightly folded. Reconstruction methods can produce geometric artifacts such as mesh self-intersections and collisions between cortical surfaces, and although recent deep learning methods have reduced reconstruction time from hours to minutes, these artifacts persist. We propose SimCortex v2, a deep learning framework for simultaneous reconstruction of the left and right WM and pial surfaces from T1-weighted MRI. SimCortex v2 estimates topologically correct initial surfaces from a volumetric segmentation and refines all four jointly using multi-scale stationary velocity fields predicted by a ribbon-conditioned, U-Net-like network. We evaluated SimCortex v2 on 560 cases from 14 cohorts, thirteen of them unseen during training, spanning ages 6-89, healthy and clinical populations, and scanners from three vendors. SimCortex v2 matched the surface-distance accuracy of the strongest baseline (average symmetric surface distance 0.253 mm) while showing no detected inter-surface collision in 92.14% of cases and the lowest self-intersection fraction (0.044%) among learning-based methods, whereas every baseline produced at least one collision in every case. Source code, configuration files, pretrained weights, preprocessed data, and the exact evaluation splits are publicly released.