Retrospective motion artifact correction of structural MRI images using deep learning improves the quality of cortical surface reconstructions

Neuroimage. 2021 Apr 15;230:117756. doi: 10.1016/j.neuroimage.2021.117756. Epub 2021 Jan 15.


Head motion during MRI acquisition presents significant challenges for neuroimaging analyses. In this work, we present a retrospective motion correction framework built on a Fourier domain motion simulation model combined with established 3D convolutional neural network (CNN) architectures. Quantitative evaluation metrics were used to validate the method on three separate multi-site datasets. The 3D CNN was trained using motion-free images that were corrupted using simulated artifacts. CNN based correction successfully diminished the severity of artifacts on real motion affected data on a separate test dataset as measured by significant improvements in image quality metrics compared to a minimal motion reference image. On the test set of 13 image pairs, the mean peak signal-to-noise-ratio was improved from 31.7 to 33.3 dB. Furthermore, improvements in cortical surface reconstruction quality were demonstrated using a blinded manual quality assessment on the Parkinson's Progression Markers Initiative (PPMI) dataset. Upon applying the correction algorithm, out of a total of 617 images, the number of quality control failures was reduced from 61 to 38. On this same dataset, we investigated whether motion correction resulted in a more statistically significant relationship between cortical thickness and Parkinson's disease. Before correction, significant cortical thinning was found to be restricted to limited regions within the temporal and frontal lobes. After correction, there was found to be more widespread and significant cortical thinning bilaterally across the temporal lobes and frontal cortex. Our results highlight the utility of image domain motion correction for use in studies with a high prevalence of motion artifacts, such as studies of movement disorders as well as infant and pediatric subjects.

Keywords: Cortical surface; Cortical thickness; Image quality; Motion artifact; Parkinson's disease; T1.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adolescent
  • Adult
  • Artifacts*
  • Autistic Disorder / diagnostic imaging
  • Cerebral Cortex / diagnostic imaging*
  • Child
  • Databases, Factual / standards
  • Deep Learning / standards*
  • Female
  • Humans
  • Image Processing, Computer-Assisted / methods
  • Image Processing, Computer-Assisted / standards*
  • Magnetic Resonance Imaging / methods
  • Magnetic Resonance Imaging / standards*
  • Male
  • Middle Aged
  • Motion*
  • Retrospective Studies
  • Young Adult