Fast surface reconstruction of human brain MRI: benchmarking deep-learning based morphometry tools

Time efficient and reliable pipelines for quantitative evaluation of structural brain MRI are essential to utilize the potential of morphometry tools for large scale research projects as well as to pave the path towards future clinical applications. In our work, we have explored this idea by evaluating three deep learning models for brain segmentation and cortex parcellation (DeepSCAN, FastSurferCNN and QuickNAT) as input for an 11-min surface reconstruction pipeline adapted from the well studied open source software package FreeSurfer. Performance was assessed using both, large publicly available human MRI datasets and a synthetic dataset with known metrics and reference surfaces. Evaluation criteria included closeness to the surface reconstruction by FreeSurfer’s full recon-all pipeline, reproducibility within same-session rescans, performance stability across a wide age range, sensitivity to variations of the grey-white contrast in the MRI and accuracy regarding metrics of synthetic surfaces. Metrics derived from the DeepSCAN-based pipeline demonstrated the highest agreement with FreeSurfer in the human data and the greatest fidelity to the expected metrics in the synthetic dataset. Our findings identify the DeepSCAN-based surface reconstruction pipeline as a rapid, yet reliable alternative to established research-grade structural MRI processing. Time expenditure and reliability suggest it is suitable for research applications with high-throughput requirements. This is an essential first step towards necessary subsequent studies aimed at evaluating robustness, pathological variability, and utility in the context of clinical diagnostics.