Open-source MRI-informed computational model of human cortical folding

Abstract

The human cerebral cortex, initially smooth, progressively folds during fetal brain development in utero, giving rise to cortical convolutions. Atypical cortical folding patterns can be associated with neurodevelopmental and neurological disorders. To better understand these conditions, it is crucial to first examine the factors governing healthy cortical folding. Computational modeling provides a powerful way for this purpose and has already helped understanding the influence of key biomechanical parameters on the folding pattern. However, most existing models use simplified geometries, limiting calibration and validation with fetal and neonatal brain Magnetic Resonance Imaging (MRI) and neglecting the influence of initial geometry on fold development. On the other hand, simulations on realistic brain geometries introduce additional challenges, including collision handling, fold characterization, and additional computational cost. Furthermore, model parameters are often difficult to interpret, complicating comparison, clinical translation, and calibration. Finally, computational models of cortical folding also remain rarely accessible. In this work, we introduce a novel computational model of cortical folding, developed using the open-source code FEniCS to simulate folding on a whole-brain geometry generated from fetal MRI data. We also propose a modular, interpretable, and scalable simulation framework built around this computational model and openly available to the community. It uses fetal MRI data to generate realistic input brain meshes and estimate key biomechanical parameters such as cortical growth rate. The framework also integrates a spectral metric for cortical surface analysis to optimize folding pattern predictions from an healthy fetal MRI dataset.