CortexODE: Learning Cortical Surface Reconstruction by Neural ODEs

Ma Q, Li L, Robinson EC, Kainz B, Rueckert D, Alansary A (2023)

Publication Type: Journal article

Publication year: 2023

Journal

IEEE Transactions on Medical Imaging Institute of Electrical and Electronics Engineers (IEEE)

Book Volume: 42

Pages Range: 430-443

Journal Issue: 2

DOI: 10.1109/TMI.2022.3206221

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.

Involved external institutions

Imperial College London / The Imperial College of Science, Technology and Medicine GB United Kingdom (GB) King’s College London GB United Kingdom (GB)

How to cite

APA:

Ma, Q., Li, L., Robinson, E.C., Kainz, B., Rueckert, D., & Alansary, A. (2023). CortexODE: Learning Cortical Surface Reconstruction by Neural ODEs. IEEE Transactions on Medical Imaging, 42(2), 430-443. https://dx.doi.org/10.1109/TMI.2022.3206221

MLA:

Ma, Qiang, et al. "CortexODE: Learning Cortical Surface Reconstruction by Neural ODEs." IEEE Transactions on Medical Imaging 42.2 (2023): 430-443.

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