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The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction

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
doi: https://doi.org/10.1101/125526
Antonios Makropoulos
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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  • For correspondence: a.makropoulos11@imperial.ac.uk
Emma C. Robinson
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Andreas Schuh
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Robert Wright
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Sean Fitzgibbon
cFMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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Jelena Bozek
dFaculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia.
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Serena J. Counsell
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Johannes Steinweg
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Jonathan Passerat-Palmbach
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Gregor Lenz
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Filippo Mortari
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Tencho Tenev
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Eugene P. Duff
cFMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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Matteo Bastiani
cFMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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Lucilio Cordero-Grande
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Emer Hughes
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Nora Tusor
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Jacques-Donald Tournier
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Jana Hutter
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Anthony N. Price
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Maria Murgasova
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Christopher Kelly
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Mary A. Rutherford
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Stephen M. Smith
cFMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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A. David Edwards
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Joseph V. Hajnal
bCentre for the Developing Brain, Division of Imaging Sciences and Biomedical Engineering, King’s College London, London, United Kingdom.
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Mark Jenkinson
cFMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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Daniel Rueckert
aBiomedical Image Analysis Group, Department of Computing, Imperial College London, London, United Kingdom.
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Abstract

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 WUMINN Human Connectome Project and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processingmechanisms, genetic 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 of neonatal subjects, 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 fully automatically processed; generating cortical surface models that are topologically and anatomically correct. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, and support the modelling of emerging patterns of brain connectivity.

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Posted April 10, 2017.
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The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction
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
bioRxiv 125526; doi: https://doi.org/10.1101/125526
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The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction
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
bioRxiv 125526; doi: https://doi.org/10.1101/125526

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