Re: [Freesurfer] Freeview aborts under centos6

2017-09-21 Thread Markus Gschwind
pefully freeview will run... or at least throw a > different error > > best > Andrew > > From: Hoopes, Andrew > Sent: Tuesday, September 19, 2017 1:56 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Freeview aborts under centos6

Re: [Freesurfer] Freeview aborts under centos6

2017-09-19 Thread Markus Gschwind
Hi Andrew, Thank you! Here is the output of bugr > [gschwind@login1 ~]$ bugr > Cut-and-paste the following info into your FreeSurfer problem report: > - > FREESURFER_HOME: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64 > Bui

Re: [Freesurfer] Freeview aborts under centos6

2017-09-19 Thread Hoopes, Andrew
Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall of vtk might work, because those shared objects that we distribute are usually sym-linked Can you also send the fs buildstamp? You can get this by running the command ‘bugr’ after sourcing freesurfer Andrew On Sep

Re: [Freesurfer] Freeview aborts under centos6

2017-09-19 Thread Markus Gschwind
Dear Andrew, after the System admin executed your proposed commands, it stays the same, Freeview aborts. Is there anything else we could try? Thank you and best wishes, Markus 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew : > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESUR

Re: [Freesurfer] Freeview aborts under centos6

2017-09-15 Thread Markus Gschwind
Thanks, I gave this to the system admin as I do not ave the sudo rights. I’ll come back! Best, Markus > On 15 Sep 2017, at 20:06, Hoopes, Andrew wrote: > > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup the shared objects > mv l

Re: [Freesurfer] Freeview aborts under centos6

2017-09-15 Thread Hoopes, Andrew
Hm okay thanks - I’m curious what happens when you run: cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.s

Re: [Freesurfer] Freeview aborts under centos6

2017-09-15 Thread Markus Gschwind
Dear Andrew, The command gives this result: [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< > $LD_LIBRARY_PATH) | grep libvtkverdict.so > /sbin/ldconfig: Can't stat > /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No > such file or directory > /sbin/ldconfig: /

Re: [Freesurfer] Freeview aborts under centos6

2017-09-15 Thread Hoopes, Andrew
Hi Markus, What is the output when you run the following: (this will list libraries you have access to) /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so best, Andrew On Sep 15, 2017, at 3:33 AM, Markus Gschwind mailto:markus.gschw...@gmail.com>> wrote: Hi ex

[Freesurfer] Freeview aborts under centos6

2017-09-15 Thread Markus Gschwind
Dear experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$ fr

[Freesurfer] Freeview aborts under centos6

2017-09-15 Thread Markus Gschwind
Hi experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$ free