Fmriprep masking failure

fmriprep
#1

I’ve got a run with a brain mask that appears to be failing badly, as you can see in the image below. I’m not sure exactly where things are going wrong. Here’s a link to a zip file containing the subjects report:https://drive.google.com/open?id=1p_bcPRybbt8s0MBUYtW0O9eH-v2eMlo_

I’ve also got the work directory for that run saved which I can share if it will help diagnose the issue.

#2

Ugh, even the least horrible masks are still horrible!

Does this dataset contain SBRefs? Could be an instance of https://github.com/poldracklab/fmriprep/issues/1684

#3

Nope, no SBRefs, it does have field maps, but the orientation information on those matches the functional.