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Geometric Deep Learning of the Human Connectome Project Multimodal Cortical Parcellation

Part of the Lecture Notes in Computer Science book series (LNIP,volume 13001)


Understanding the topographic heterogeneity of cortical organisation is an essential step towards precision modelling of neuropsychiatric disorders. While many cortical parcellation schemes have been proposed, few attempt to model inter-subject variability. For those that do, most have been proposed for high-resolution research quality data, without exploration of how well they generalise to clinical quality scans. In this paper, we benchmark and ensemble four different geometric deep learning models on the task of learning the Human Connectome Project (HCP) multimodal cortical parcellation. We employ Monte Carlo dropout to investigate model uncertainty with a view to propagate these labels to new datasets. Models achieved an overall Dice overlap ratio of \({>}0.85\,\pm \,0.02\). Regions with the highest mean and lowest variance included V1 and areas within the parietal lobe, and regions with the lowest mean and highest variance included areas within the medial frontal lobe, lateral occipital pole and insula. Qualitatively, our results suggest that more work is needed before geometric deep learning methods are capable of fully capturing atypical cortical topographies such as those seen in area 55b. However, information about topographic variability between participants was encoded in vertex-wise uncertainty maps, suggesting a potential avenue for projection of this multimodal parcellation to new datasets with limited functional MRI, such as the UK Biobank.


  • Human connectome project
  • Geometric deep learning
  • Cortical parcellation

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Data were provided by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University [31].

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Correspondence to Logan Z. J. Williams .

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Williams, L.Z.J., Fawaz, A., Glasser, M.F., Edwards, A.D., Robinson, E.C. (2021). Geometric Deep Learning of the Human Connectome Project Multimodal Cortical Parcellation. In: Abdulkadir, A., et al. Machine Learning in Clinical Neuroimaging. MLCN 2021. Lecture Notes in Computer Science(), vol 13001. Springer, Cham.

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