Hi, I haven’t done this with the output of FMRIPREP, but have encountered the same registration issue with the HCP data (which is already registered to MNI space). For that, their solution is to use link to a identity matrix and the standard brain:
ln -s $FSLDIR/etc/flirtsch/ident.mat $feat/reg/example_func2standard.mat
ln -s $FSLDIR/etc/flirtsch/ident.mat $feat/reg/standard2example_func.mat
ln -s $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz $feat/reg/standard.nii.gz
https://wiki.humanconnectome.org/display/PublicData/Advice+for+FEAT+Analysis+of+HCP+task+fMRI+data
This seems to work ok for us, and I suspect a similar solution could work with other datasets that are already registered.
Best,
David