{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/the-developing-human-connectome-project-a","title":"The Developing Human Connectome Project: A Fast Deep Learning-based Pipeline for Neonatal Cortical Surface Reconstruction","arxiv_id":"2405.08783","date":"2024-05-14","proceeding":null,"authors":["Qiang Ma","Kaili Liang","Liu Li","Saga Masui","Yourong Guo","Chiara Nosarti","Emma C. Robinson","Bernhard Kainz","Daniel Rueckert"],"abstract":"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 hours 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 seconds 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.","url_abs":"https://arxiv.org/abs/2405.08783v2","url_pdf":"https://arxiv.org/pdf/2405.08783v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"the-developing-human-connectome-project-a","repo_url":"https://github.com/m-qiang/dhcp-dl-neonatal","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":null,"task_name":"GPU"},{"task_slug":"surface-reconstruction","task_name":"Surface Reconstruction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}