Re: [Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

Hi Lauri

I think you forgot to attach the logs

Bruce

On Thu, 10 Dec 2015, Tuominen, Lauri Johannes wrote:

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