Thanks for sending the reports. The distortions you are seeing in MRIQC are due to very rough registration that MRIQC is performing to calculate one of its metrics. It is not indicative of FMRIPREP performance since FMRIPREP uses other strategies.
Nonetheless I see that the bold-T1w coregistration in FMRIPREP reports is suboptimal. This is likely due to susceptibility distortions and low tissue contrast. There are few of things you could try (in order of most likely to work):
- Run it again with FMRIPREP 1.0.2 - there were many improvements since rc2
- Run it with FMRIPREP 1.0.2 turning on the
- Run it with FMRIPREP 1.0.2 turning on
- Run it with FMRIPREP 1.0.2 turning on both
Please let us know what you found so we could make FMRIPREP better!