Dear Antonin,
Thank you for your reply and clarification at
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055331.html
. I was changing the recon-all file in the subject folder rather than the one
in the freesurfer/bin folder. The command recon-all now runs to completion
Dear Shadia,
please check, that you really edited your recon.all, as I suggested in my
previous mail. Your recon-all file is located here:
/home/s1163658/freesurferv60/bin/recon-all
According to your recon-all.log, there is still an ln -s command invoked (which
should be replaced by cp command)
Dear Shadia,
There are 2 spots in recon-all where symbolic link is created.
The first you can overcome by:
find following line in your recon-all:
set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)
and replace it by
set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix
