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The Developing Human Connectome Project: a minimal processing pipeline for neonatal cortical surface reconstruction

Makropoulos, Antonios; Robinson, Emma C; Schuh, Andreas; Wright, Robert; Fitzgibbon, Sean; Bozek, Jelena; Counsell, Serena J; Steinweg, Johannes; Passerat-Palmbach, Jonathan; Lenz, Gregor; Mortari, Filippo; Tenev, Tencho; Duff, Eugene P; Bastiani, Matteo; Cordero-Grande, Lucilio; Hughes, Emer; Tusor, Nora; Tournier, Jacques-Donald; Hutter, Jana; Price, Anthony N; Murgasova, Maria; Kelly, Christopher; Rutherford, Mary A; Smith, Stephen M; Edwards, A. David; Hajnal, Joseph V; Jenkinson, Mark; Rueckert, Daniel


Antonios Makropoulos

Emma C Robinson

Andreas Schuh

Robert Wright

Sean Fitzgibbon

Jelena Bozek

Serena J Counsell

Johannes Steinweg

Jonathan Passerat-Palmbach

Gregor Lenz

Filippo Mortari

Tencho Tenev

Eugene P Duff

Matteo Bastiani

Lucilio Cordero-Grande

Emer Hughes

Nora Tusor

Jacques-Donald Tournier

Jana Hutter

Anthony N Price

Maria Murgasova

Christopher Kelly

Mary A Rutherford

Stephen M Smith

A. David Edwards

Joseph V Hajnal

Mark Jenkinson

Daniel Rueckert


The Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity.


Makropoulos, A., Robinson, E. C., Schuh, A., Wright, R., Fitzgibbon, S., Bozek, J., …Rueckert, D. (2018). The Developing Human Connectome Project: a minimal processing pipeline for neonatal cortical surface reconstruction. NeuroImage, 173, 88-112.

Journal Article Type Article
Acceptance Date Jan 21, 2018
Online Publication Date Jan 31, 2018
Publication Date Jun 30, 2018
Deposit Date Oct 12, 2018
Publicly Available Date Feb 1, 2019
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 173
Pages 88-112
Public URL
Publisher URL


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