From Low Field to High Value: Robust Cortical Mapping from Low-Field MRI

• URL: http://arxiv.org/abs/2505.12228v1
• Date: Sun, 18 May 2025 04:24:18 GMT
• Title: From Low Field to High Value: Robust Cortical Mapping from Low-Field MRI
• Authors: Karthik Gopinath, Annabel Sorby-Adams, Jonathan W. Ramirez, Dina Zemlyanker, Jennifer Guo, David Hunt, Christine L. Mac Donald, C. Dirk Keene, Timothy Coalson, Matthew F. Glasser, David Van Essen, Matthew S. Rosen, Oula Puonti, W. Taylor Kimberly, Juan Eugenio Iglesias,
• Abstract summary: We present a machine learning method for 3D reconstruction and analysis of portable LF-MRI.<n>We use a 3D U-Net trained on synthetic LF-MRI to predict signed distance functions of cortical surfaces.<n>Our method represents a step toward enabling cortical surface analysis on portable LF-MRI.
• Score: 3.341362699606649
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Three-dimensional reconstruction of cortical surfaces from MRI for morphometric analysis is fundamental for understanding brain structure. While high-field MRI (HF-MRI) is standard in research and clinical settings, its limited availability hinders widespread use. Low-field MRI (LF-MRI), particularly portable systems, offers a cost-effective and accessible alternative. However, existing cortical surface analysis tools are optimized for high-resolution HF-MRI and struggle with the lower signal-to-noise ratio and resolution of LF-MRI. In this work, we present a machine learning method for 3D reconstruction and analysis of portable LF-MRI across a range of contrasts and resolutions. Our method works "out of the box" without retraining. It uses a 3D U-Net trained on synthetic LF-MRI to predict signed distance functions of cortical surfaces, followed by geometric processing to ensure topological accuracy. We evaluate our method using paired HF/LF-MRI scans of the same subjects, showing that LF-MRI surface reconstruction accuracy depends on acquisition parameters, including contrast type (T1 vs T2), orientation (axial vs isotropic), and resolution. A 3mm isotropic T2-weighted scan acquired in under 4 minutes, yields strong agreement with HF-derived surfaces: surface area correlates at r=0.96, cortical parcellations reach Dice=0.98, and gray matter volume achieves r=0.93. Cortical thickness remains more challenging with correlations up to r=0.70, reflecting the difficulty of sub-mm precision with 3mm voxels. We further validate our method on challenging postmortem LF-MRI, demonstrating its robustness. Our method represents a step toward enabling cortical surface analysis on portable LF-MRI. Code is available at https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAny

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