Thank you for the help and for getting back to me,

After using the custom-fill option and labelling the central sulcus (yellow), I've been running the following code:
"mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central
subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg".

Which is followed by
"mris_ca_label subject ?h subject/surf/?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot" or "recon-all -make all -subject". For some reason, I don't see any difference in the subject Destrieux-labelling (the incorrect shift is still there) and I suspect that I'm not doing this correctly. Would it be possible for you to check if I'm using the wrong syntax or if I might have missed out on some parts necessary for this solution to work? 

Kind regards,

Carl