CortexODE: learning cortical surface reconstruction by neural ODEs
File(s)
Accepted version
Author(s)
Type
Journal Article
Abstract
We present CortexODE, a deep learning framework for cortical surface reconstruction. CortexODE leverages neural ordinary differential equations (ODEs) to deform an input surface into a target shape by learning a diffeomorphic flow. The trajectories of the points on the surface are modeled as ODEs, where the derivatives of their coordinates are parameterized via a learnable Lipschitz-continuous deformation network. This provides theoretical guarantees for the prevention of self-intersections. CortexODE can be integrated to an automatic learning-based pipeline, which reconstructs cortical surfaces efficiently in less than 5 seconds. The pipeline utilizes a 3D U-Net to predict a white matter segmentation from brain Magnetic Resonance Imaging (MRI) scans, and further generates a signed distance function that represents an initial surface. Fast topology correction is introduced to guarantee homeomorphism to a sphere. Following the isosurface extraction step, two CortexODE models are trained to deform the initial surface to white matter and pial surfaces respectively. The proposed pipeline is evaluated on large-scale neuroimage datasets in various age groups including neonates (25-45 weeks), young adults (22-36 years) and elderly subjects (55-90 years). Our experiments demonstrate that the CortexODE-based pipeline can achieve less than 0.2mm average geometric error while being orders of magnitude faster compared to conventional processing pipelines.
Date Issued
2023-02
Date Acceptance
2022-09-02
Citation
IEEE Transactions on Medical Imaging, 2023, 42 (2), pp.430-443
ISSN
0278-0062
Publisher
Institute of Electrical and Electronics Engineers
Start Page
430
End Page
443
Journal / Book Title
IEEE Transactions on Medical Imaging
Volume
42
Issue
2
Copyright Statement
Copyright © 2023 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Identifier
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000934156000010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=a2bf6146997ec60c407a63945d4e92bb
Subjects
BRAIN
Brain MRI
Computer Science
Computer Science, Interdisciplinary Applications
cortical surface reconstruction
Engineering
Engineering, Biomedical
Engineering, Electrical & Electronic
FLOWS
FRAMEWORK
geometric deep learning
HUMAN CONNECTOME PROJECT
Image reconstruction
Imaging Science & Photographic Technology
Life Sciences & Biomedicine
Magnetic resonance imaging
neural ODE
Pipelines
Radiology, Nuclear Medicine & Medical Imaging
Science & Technology
Strain
Surface morphology
Surface reconstruction
Surface treatment
Technology
THICKNESS
TOPOLOGY-CORRECTION
VOLUME
Publication Status
Published
Date Publish Online
2022-09-12