The Developing Human Connectome Project: A fast deep learning-based pipeline for neonatal cortical surface reconstruction

The Developing Human Connectome Project (dHCP) aims to explore developmental patterns of the human brain during the perinatal period. An automated processing pipeline has been developed to extract high-quality cortical surfaces from structural brain magnetic resonance (MR) images for the dHCP neonatal dataset. However, the current implementation of the pipeline requires more than 6.5 h to process a single MRI scan, making it expensive for large-scale neuroimaging studies. In this paper, we propose a fast deep learning (DL) based pipeline for dHCP neonatal cortical surface reconstruction, incorporating DL-based brain extraction, cortical surface reconstruction and spherical projection, as well as GPU-accelerated cortical surface inflation and cortical feature estimation. We introduce a multiscale deformation network to learn diffeomorphic cortical surface reconstruction end-to-end from T2-weighted brain MRI. A fast unsupervised spherical mapping approach is integrated to minimize metric distortions between cortical surfaces and projected spheres. The entire workflow of our DL-based dHCP pipeline completes within only 24 s on a modern GPU, which is nearly 1000 times faster than the original dHCP pipeline. The qualitative assessment demonstrates that for 82.5% of the test samples, the cortical surfaces reconstructed by our DL-based pipeline achieve superior (54.2%) or equal (28.3%) surface quality compared to the original dHCP pipeline. •A deep learning-based neuroimage processing pipeline is presented for neonatal cortical surface reconstruction in the Developing Human Connectome Project (dHCP).•A multiscale deformation network is introduced to learn diffeomorphic cortical surface reconstruction end-to-end from neonatal brain MRI.•The entire workflow of our pipeline only requires 24 s on a modern GPU.•Our pipeline achieves superior cortical surface quality while being nearly 1000 times faster than the previous dHCP structural pipeline.