I have the same question! I have issue A (brightness “ring” around the brain, and some large bright vs. dark patterns) in fMRIprep 20.2.0, but add some additional context.
I have the same subjects run through fMRIprep 1.2.6-1 and fMRIprep 20.2.0 and the older version of fMRIprep does not show issues that look like this in the reports. One additional change with the newer version is the additional of a pediatric template as an output space, but I didn’t expect this change to result from that. Both have pre-run (the same) Freesurfer input. No susceptibility distortion correction applied in either case.
Is this something about the Nearest Neighbor interpolation vs. Lanczos interpolation? Did that change between versions? Or how EPIs are displayed in the report? Is this even something to be concerned about?
Command for 20.2.0:
/usr/local/miniconda/bin/fmriprep /cbica/projects/cbpd_main_data/CBPD_bids /cbica/projects/cbpd_main_data/CBPD_bids/derivatives/fmriprep_t1 participant --participant-label CBPD0172 --fs-license-file /cbica/projects/cbpd_main_data/license.txt --fs-subjects-dir /cbica/projects/cbpd_main_data/CBPD_bids/derivatives/freesurfer_t1 --bids-filter-file /cbica/projects/cbpd_main_data/CBPD_bids/derivatives/fmriprep/ses_01_CBPD0172.json --skull-strip-template MNIPediatricAsym:res-1:cohort-2 --output-spaces MNI152NLin6Asym T1w MNIPediatricAsym:res-1:cohort-2 --ignore sbref --verbose --nthreads 8 -w /tmp
Command for 1.2.6-1
/usr/local/miniconda/bin/fmriprep /cbica/projects/cbpd_main_data/CBPD_bids /cbica/projects/cbpd_main_data/CBPD_bids/derivatives/ participant -w /cbica/projects/cbpd_main_data/fmriprep_wd/ --participant-label sub-CBPD0172 --fs-license-file /home/utooley/license.txt --output-space T1w template --ignore fieldmaps sbref --nthreads 1