TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces

Andrew Hoopes, Juan Eugenio Iglesias, Bruce Fischl, Douglas Greve, Adrian V Dalca

Keywords: Cortical Surface Reconstruction, Topology, Geometric Deep-Learning

TL;DR: We introduce TopoFit, a learning-based method to rapidly fit topologically-correct surfaces to the cerebral cortex.

Abstract: Mesh-based reconstruction of the cerebral cortex is a fundamental component in brain image analysis. Classical, iterative pipelines for cortical modeling are robust but often time-consuming, mostly due to expensive procedures that involve topology correction and spherical mapping. Recent attempts to address reconstruction with machine learning methods have accelerated some components in these pipelines, but these methods still require slow processing steps to enforce topological constraints that comply with known anatomical structure. In this work, we introduce a novel learning-based strategy, TopoFit, which rapidly fits a topologically-correct surface to the white-matter tissue boundary. We design a joint network, employing image and graph convolutions and an efficient symmetric distance loss, to learn to predict accurate deformations that map a template mesh to subject-specific anatomy. This technique encompasses the work of current mesh correction, fine-tuning, and inflation processes and, as a result, offers a $150\times$ faster solution to cortical surface reconstruction compared to traditional approaches. We demonstrate that TopoFit is $1.8\times$ more accurate than the current state-of-the-art deep-learning strategy, and it is robust to common failure modes, such as white-matter tissue hypointensities.

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Paper Type: methodological development

Primary Subject Area: Segmentation

Secondary Subject Area: Image Registration

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