The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files
/usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
The former exists where it should, the latter does not exist at that location, although it can be downloaded from
http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads
and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e.
/usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca
Could someone with the appropriate permissions please copy that file to where recon-all expects to find it?
Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?