Thanks for your reply! I will test the -d flag using fmriprep:unstable.
Actually, I wasn’t planning to bring this up here, but I discovered the -d flag bug while investigating another issue—the BOLD mask output from fMRIPrep appears incorrect, even though the corresponding xfm.txt is correct. See the screenshots below:
(Blue represents the mask output by fMRIPrep, while purple is the mask I calculated using the same
xfm.txt and the T1w mask.)
After reading these posts (Brain mask generation in fMRIPrep, fMRIPrep BOLD brain mask issue), it seems that others have managed to replace incorrect brain masks in intermediate steps and then re-run fMRIPrep.
So, I attempted to use --level minimal, generate the brain mask myself, and finally use -d to bring the new bold mask, but now I’m encountering this bug.
Do you have any thoughts on the bold mask issue? Or should I open a new topic and tag you there?