Dear Patricia,

this is I suppose the last issue concerning symbolic links, related with part of code starting with following comment:

# if fsaverage is not in subjects dir, put it there

I think that the most straightforward  solution of this issue is to manually copy the fsaverage subject to $SUBJECTS_DIR before invocation of recon-all.

Antonin

forgot to attach the printscreen

2017-04-06 9:49 GMT+02:00 Patr?cia Klobu?iakov? < patricia.klobusiakova@gmail.com>:

Hi Antonin,

I edited recon-all file, but another error was reported. This error concerns symbolic links, too. Is there any way I could make it work on this virtual machine? I coud try to substitute all ln commands with cp or something like that.

Thanks.

Patricia

2017-04-04 13:43 GMT+02:00 Antonin Skoch ansk@ikem.cz:

...

Dear Patricia,

see this thread:

freesurfer@nmr.mgh.harvard.edu/msg51797.html" title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html" target="_blank">http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html

Your working directory probably resides on the filesystem which does not support symbolic links. You probably could workaround this by editing your recon-all and replace line

set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) by

set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix)

Antonin Skoch

Hello FreeSurfer Developers,  I have installed Freesurfer on Windows using VMware - CentOS 64-bit (the one from FSLuser Linux installation).  Everytime I run recon-all, there is an error.  The same error occurs  when I try to rum mri2mesh command in SIMNIBS toolbox which uses Fresurfer (recon-all), too. I'm sending screenshots and logfile attached.   Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux fslvm6.localdomain 2.6.32-431.5.1.el6.x86_64          #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux  Thanks for your help.

Best,  Patricia