Assessing methods for geometric distortion compensation in 7T gradient echo fMRI data [article]

Michael-Paul Schallmo, Kimberly B Weldon, Scott R Sponheim, Cheryl A Olman
2020 bioRxiv   pre-print
Echo planar imaging (EPI) is widely used in functional and diffusion-weighted MRI, but suffers from significant geometric distortions in the phase encoding direction caused by inhomogeneities in the static magnetic field (B0). This is a particular challenge for EPI at very high field (7T and above), as distortion increases with higher field strength. A number of techniques for correcting geometric distortion exist, including those based on B0 field mapping and acquiring EPI scans with opposite
more » ... cans with opposite phase encoding directions. However, few quantitative comparisons of distortion compensation methods have been performed using EPI data from the human brain, and even fewer at very high field. In the current study, we compared geometric distortion compensation using B0 field maps and opposite phase encoding scans implemented in two different software packages (FSL and AFNI) applied to 7T gradient echo EPI data from 31 human participants. We assessed the quality of distortion compensation by quantifying the degree of alignment to a T1-weighted anatomical reference scan using Dice coefficients and mutual information. We found that the best distortion compensation was achieved in our dataset using gradient echo scans with opposite phase encoding directions to map the distortion, as compared to B0 field maps or spin echo opposite phase encoding scans. Performance between FSL and AFNI was equivalent. While the ideal geometric distortion compensation approach may vary due to methodological differences across experiments, this study provides a framework for researchers to assess the quality of different distortion compensation methods in their own work.
doi:10.1101/2020.07.02.184515 fatcat:2zajeokxnzdwdotw3qe775lkti