[Freesurfer] recon-all exited with errors

2013-09-03 Thread Troebinger, Luzia
Hi all, I posted a message regarding this problem a while ago, but still not resolved. Basically, freesurfer exits with errors in the final (autorecon-3) stages, because of what must be a problem with the symbolic link lh.EC_average. The link is created as should be, but I get an error message

[Freesurfer] error for autorecon3

2013-08-19 Thread Troebinger, Luzia
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

[Freesurfer] head/face surface extraction

2013-02-04 Thread Troebinger, Luzia
Hi, I have what I suppose is a slightly unusual question - is it possible to get the head/face shape from a subject's MRI using FreeSurfer? I've only ever used it to get the cortical surface, but was wondering if I could somehow extract the head/face shape, as well. Best Luzia