首个可直接处理任意临床脑影像的皮层表面重建方法,无需重新训练。
End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images
- 用合成数据训练神经网络,直接从任意分辨率和对比度图像中重建皮层表面。
- 相比现有方法,皮层厚度误差降低50%(0.50→0.24 mm),更准确捕捉老化导致的变薄模式。
- 适合大规模临床研究,尤其适用于难以入组的研究人群。
基于表面的皮层分析在多种神经影像任务中具有价值,如空间标准化、区域划分和灰质厚度估计。然而,大多数皮层表面估计工具仅适用于至少1 mm各向同性分辨率的扫描,且针对特定磁共振对比(常为T1加权)。这限制了其在多数临床扫描中的应用,因为临床扫描在对比度和分辨率上差异极大。本文使用合成领域随机化数据,训练首个能够从任意对比度和分辨率图像中显式重建皮层表面的神经网络,且无需重新训练。该方法先将模板网格变形至白质表面,保证拓扑正确性;再进一步变形以估计灰质表面。我们在ADNI和一个大型临床数据集(n=1,332)上与RAC(目前唯一能处理异构临床扫描的隐式重建方法)进行比较,结果显示皮层厚度误差降低约50%(从0.50降至0.24 mm),且对高分辨率T1w扫描中由FreeSurfer检测到的老化相关皮层变薄模式恢复更优。本方法实现临床扫描的快速、高精度表面重建,使大规模研究(远超研究场景可行性)和难招募人群研究成为可能。代码已公开于https://github.com/simnibs/brainnet。
原文摘要 · Abstract (English)
Surface-based cortical analysis is valuable for a variety of neuroimaging tasks, such as spatial normalization, parcellation, and gray matter (GM) thickness estimation. However, most tools for estimating cortical surfaces work exclusively on scans with at least 1 mm isotropic resolution and are tuned to a specific magnetic resonance (MR) contrast, often T1-weighted (T1w). This precludes application using most clinical MR scans, which are very heterogeneous in terms of contrast and resolution. Here, we use synthetic domain-randomized data to train the first neural network for explicit estimation of cortical surfaces from scans of any contrast and resolution, without retraining. Our method deforms a template mesh to the white matter (WM) surface, which guarantees topological correctness. This mesh is further deformed to estimate the GM surface. We compare our method to recon-all-clinical (RAC), an implicit surface reconstruction method which is currently the only other tool capable of processing heterogeneous clinical MR scans, on ADNI and a large clinical dataset (n=1,332). We show a approximately 50 % reduction in cortical thickness error (from 0.50 to 0.24 mm) with respect to RAC and better recovery of the aging-related cortical thinning patterns detected by FreeSurfer on high-resolution T1w scans. Our method enables fast and accurate surface reconstruction of clinical scans, allowing studies (1) with sample sizes far beyond what is feasible in a research setting, and (2) of clinical populations that are difficult to enroll in research studies. The code is publicly available at https://github.com/simnibs/brainnet.
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