What is the output of the first command? And if you bring up the ?h.sphere.reg does it align better with the atlas? You can use mrisp_paint or just look at fsaverage on the sphere

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Trolle, Carl
Sent: Wednesday, August 3, 2022 9:25 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

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