Surface Masked AutoEncoder: Self-Supervision for Cortical Imaging Data

Self-supervision has been widely explored as a means of addressing the lack of inductive biases in vision transformer architectures, which limits generalisation when networks are trained on small datasets. This is crucial in the context of cortical imaging, where phenotypes are complex and heterogeneous, but the available datasets are limited in size. This paper builds upon recent advancements in translating vision transformers to surface meshes and investigates the potential of Masked AutoEncoder (MAE) self-supervision for cortical surface learning. By reconstructing surface data from a masked version of the input, the proposed method effectively models cortical structure to learn strong representations that translate to improved performance in downstream tasks. We evaluate our approach on cortical phenotype regression using the developing Human Connectome Project (dHCP) and demonstrate that pre-training leads to a 26\% improvement in performance, with an 80\% faster convergence, compared to models trained from scratch. Furthermore, we establish that pre-training vision transformer models on large datasets, such as the UK Biobank (UKB), enables the acquisition of robust representations for finetuning in low-data scenarios. Our code and pre-trained models are publicly available at \url{https://github.com/metrics-lab/surface-vision-transformers}.