Fmriprep weird EPI-T1 registration artifact/problems

I have opened https://github.com/poldracklab/fmriprep/issues/1538 to follow up on this. Please feel invited to contribute to fMRIPrep with the appropriate edit to the reports (it basically entails editing these lines:
https://github.com/poldracklab/fmriprep/blob/6dd2d4e4d91b42f8ae8d912698f14abd39ece782/fmriprep/viz/config.json#L123
https://github.com/poldracklab/fmriprep/blob/6dd2d4e4d91b42f8ae8d912698f14abd39ece782/fmriprep/viz/config.json#L117
https://github.com/poldracklab/fmriprep/blob/6dd2d4e4d91b42f8ae8d912698f14abd39ece782/fmriprep/viz/config.json#L111
https://github.com/poldracklab/fmriprep/blob/6dd2d4e4d91b42f8ae8d912698f14abd39ece782/fmriprep/viz/config.json#L105
)