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:

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

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