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.klobusiak...@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 <a...@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
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