Journal
IEEE TRANSACTIONS ON MEDICAL IMAGING
Volume 42, Issue 2, Pages 430-443Publisher
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/TMI.2022.3206221
Keywords
Surface reconstruction; Surface treatment; Pipelines; Surface morphology; Image reconstruction; Magnetic resonance imaging; Strain; Brain MRI; cortical surface reconstruction; geometric deep learning; neural ODE
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CortexODE is a deep learning framework that uses neural ordinary differential equations (ODEs) to reconstruct cortical surfaces. By modeling the trajectories of points on the surface as ODEs and parameterizing the derivatives with a learnable deformation network, CortexODE is able to prevent self-intersections. Integrated with an automatic learning-based pipeline, CortexODE can efficiently reconstruct cortical surfaces in less than 5 seconds.
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.
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