Effect of head motion-induced artefacts on the reliability of deep learning-based whole-brain segmentation

Due to their robustness and speed, recently developed deep learning-based methods have the potential to provide a faster and hence more scalable alternative to more conventional neuroimaging analysis pipelines in terms of whole-brain segmentation based on magnetic resonance (MR) images. These methods were also shown to have higher test–retest reliability, raising the possibility that they could also exhibit superior head motion tolerance. We investigated this by comparing the effect of head motion-induced artifacts in structural MR images on the consistency of segmentation performed by FreeSurfer and recently developed deep learning-based methods to a similar extent. We used state-of-the art neural network models (FastSurferCNN and Kwyk) and developed a new whole-brain segmentation pipeline (ReSeg) to examine whether reliability depends on choice of deep learning method. Structural MRI scans were collected from 110 participants under rest and active head motion and were evaluated for image quality by radiologists. Compared to FreeSurfer, deep learning-based methods provided more consistent segmentations across different levels of image quality, suggesting that they also have the advantage of providing more reliable whole-brain segmentations of MR images corrupted by motion-induced artifacts, and provide evidence for their practical applicability in the study of brain structural alterations in health and disease.