Cortical Surface Parcellation Using Spherical Convolutional Neural Networks

Prasanna Parvathaneni, Shunxing Bao, Vishwesh Nath, Neil D. Woodward, Daniel O. Claassen, Carissa J. Cascio, David H. Zald, Yuankai Huo, Bennett A. Landman, Ilwoo Lyu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations


We present cortical surface parcellation using spherical deep convolutional neural networks. Traditional multi-atlas cortical surface parcellation requires inter-subject surface registration using geometric features with slow processing speed on a single subject (2–3 h). Moreover, even optimal surface registration does not necessarily produce optimal cortical parcellation as parcel boundaries are not fully matched to the geometric features. In this context, a choice of training features is important for accurate cortical parcellation. To utilize the networks efficiently, we propose cortical parcellation-specific input data from an irregular and complicated structure of cortical surfaces. To this end, we align ground-truth cortical parcel boundaries and use their resulting deformation fields to generate new pairs of deformed geometric features and parcellation maps. To extend the capability of the networks, we then smoothly morph cortical geometric features and parcellation maps using the intermediate deformation fields. We validate our method on 427 adult brains for 49 labels. The experimental results show that our method outperforms traditional multi-atlas and naive spherical U-Net approaches, while achieving full cortical parcellation in less than a minute.

Original languageEnglish (US)
Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings
EditorsDinggang Shen, Pew-Thian Yap, Tianming Liu, Terry M. Peters, Ali Khan, Lawrence H. Staib, Caroline Essert, Sean Zhou
Number of pages9
ISBN (Print)9783030322472
StatePublished - 2019
Externally publishedYes
Event22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019 - Shenzhen, China
Duration: Oct 13 2019Oct 17 2019

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11766 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)


  • Cortical surface parcellation
  • Spherical U-Net
  • Spherical deformation
  • Surface registration

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