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