S3Reg: Superfast Spherical Surface Registration Based on Deep Learning

Fenqiang Zhao, Zhengwang Wu, Fan Wang, Weili Lin, Shunren Xia, Dinggang Shen, Li Wang, Gang Li

Research output: Contribution to journalArticlepeer-review

16 Citations (Scopus)


Cortical surface registration is an essential step and prerequisite for surface-based neuroimaging analysis. It aligns cortical surfaces across individuals and time points to establish cross-sectional and longitudinal cortical correspondences to facilitate neuroimaging studies. Though achieving good performance, available methods are either time consuming or not flexible to extend to multiple or high dimensional features. Considering the explosive availability of large-scale and multimodal brain MRI data, fast surface registration methods that can flexibly handle multimodal features are desired. In this study, we develop a Superfast Spherical Surface Registration (S3Reg) framework for the cerebral cortex. Leveraging an end-to-end unsupervised learning strategy, S3Reg offers great flexibility in the choice of input feature sets and output similarity measures for registration, and meanwhile reduces the registration time significantly. Specifically, we exploit the powerful learning capability of spherical Convolutional Neural Network (CNN) to directly learn the deformation fields in spherical space and implement diffeomorphic design with 'scaling and squaring' layers to guarantee topology-preserving deformations. To handle the polar-distortion issue, we construct a novel spherical CNN model using three orthogonal Spherical U-Nets. Experiments are performed on two different datasets to align both adult and infant multimodal cortical features. Results demonstrate that our S3Reg shows superior or comparable performance with state-of-the-art methods, while improving the registration time from 1 min to 10 sec.

Original languageEnglish
Article number9389746
Pages (from-to)1964-1976
Number of pages13
JournalIEEE Transactions on Medical Imaging
Issue number8
Publication statusPublished - 2021 Aug

Bibliographical note

Publisher Copyright:
© 1982-2012 IEEE.


  • Surface registration
  • convolutional neural networks
  • diffeomorphism
  • spherical U-Net
  • unsupervised learning

ASJC Scopus subject areas

  • Software
  • Radiological and Ultrasound Technology
  • Computer Science Applications
  • Electrical and Electronic Engineering


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