Dear Freesurfer experts,
So, 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
P.s. Hopefully the attachments got trough this time.
Lauri Tuominen, Research Fellow A. A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division Massachusetts General Hospital 149 Thirteenth Street, Suite 2611, Charlestown, MA 02129