Hi @atersakyan, I actually did not have any problems running fMRIPrep on this file.
If you still have your working directory, delete the
fmriprep_wf/single_subject_0217ba_wf/anat_preproc_wf/brain_extraction_wf subdirectory, and see if re-running resolves the issue. It may be that the random initialization hit an unlikely error condition.
One other difference is that I used the latest releases (1.4.1), so if you get the same result as before, you can try upgrading.
Another possibility is that defacing for some reason makes the initial registration work a bit better. You could try replacing your T1w.nii.gz files with the defaced versions.