I've attached a tar of the vtk library (vtk.tar.gz). To reinstall this, the sys admin should run:

tar -xzvf vtk.tar.gz
rm -rf $FREESURFER_HOME/lib/vtk
mv vtk  $FREESURFER_HOME/lib/

after doing this, running the following command should display a bunch of symbolic links:
ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/libvtk*

If that's the case, hopefully 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

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 19, 2017, at 11:02 AM, Markus Gschwind <markus.gschwind@gmail.com<mailto:markus.gschwind@gmail.com>> wrote:

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 <AHOOPES@mgh.harvard.edu<mailto:AHOOPES@mgh.harvard.edu>>:
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.so.5.6.0 libvtkverdict.so.5.6

then do you get the same error from freeview?

-Andrew

On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschwind@gmail.com<mailto:markus.gschwind@gmail.com>> wrote:

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: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg
/sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg
/sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg
/sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg
/sbin/ldconfig: Path `/usr/lib64' given more than once
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link
libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link
/sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link


Thanks for your help!!

Markus

2017-09-15 17:49 GMT+02:00 Hoopes, Andrew <AHOOPES@mgh.harvard.edu<mailto:AHOOPES@mgh.harvard.edu>>:
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 <markus.gschwind@gmail.com<mailto:markus.gschwind@gmail.com>> wrote:

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 ~]$ freeview
Abort

When running freeview.bin it complains about a libraries error:

[gschwind@login1 ~]$ freeview.bin
freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory

I searched the archives and found this info to be given,

[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0


I then integrated this into bashrc

export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6

however, the problem persists.

Any help is highly appreciated!

Thanks you!
Markus
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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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