Artifacts in fmriprep-report html


I’m looking for some suggestions on how to go about troubleshooting these artifacts that I see in the fmriprep-report html files from fmriprep 20.2.1. These examples are all from different subjects - but happen in multiple runs somewhat randomly:

A) (brighter vs darker patterns)

B) (intensity difference?)


D) (brighter cortical vs darker subcortical)

  1. any tips on what could cause these behaviors?
  2. how are the images used as background calculated, eg for the “alignment of functional and anatomical MRI data (surface driven)” and for the “SDC” plots?

Thanks in advance!

forgot to mention: both the raw input to fMRIprep and the output look good from a manual inspection

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



Update: after looking through the final outputs, I’ve decided that the bright-dark spots aren’t directly affecting the BOLD output…but I’m still not sure why it changed. So I’d still be curious about this, because many of my subjects now have a bright “ring” around the brain (see below) in 20.2.0 that I didn’t see in the reports from 1.2.6-1.