Hi Luzia

the lh.EC_average should be a symlink to $FREESURFER_HOME/subjects/lh.EC_average

if it doesn't exist, create it with ln -s

cheers Bruce

On Mon, 19 Aug 2013, Troebinger, Luzia wrote:

Hi all,

I am trying to run recon-all on a structural for one of my subjects, but freesurfer exited with errors during the last few stages (the ones covered by autorecon-3). It appears that it is just missing some label - the problem occurs at the following stage:

painting output onto subject ME. processing subject lh.EC_average... MRISread (filename) could not open file

I've used freesurfer before, same subject directory, but didn't get this error - it appears from the path after the MRISread command that it is just the subject directory, but not the directory for this particular subject. It appears freesurfer is looking for this file, which it can't find: /home/virtualuser/freesurfer/s_sub/lh.EC_average/surf/lh.sphere.reg where /home/virtualuser/freesurfer/s_sub is my subject directory.

Can anyone advise as to how to fix this? Any help would be much appreciated.

Best Luzia