Dear Freesurfer experts,

I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but part of the occipital cortex was missing and I therefore ran the following command ( both in freesurfer6 ):

  recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib

This took care of the brain mask problem that I had with the previous recon. So I then ran on launchpad:

 recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1'

The last command exits with errors. Please find the log-files attached.

Thank you for your help!

Best,
Lauri Tuominen