Dear Andrew, So the sys admin has changed the libraries.
however, it did not change anything. Freeview aborts without comment. Below the command you asked for the result. Any other ideas? What other info would you like to get? Sorry for that persisting problem! And thanks for your help! Markus ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/libvtk* lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so -> libvtkalglib.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 -> libvtkalglib.so.5.6.0 -rwxr-xr-x 1 sagon unige 146394 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so -> libvtkCommon.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 -> libvtkCommon.so.5.6.0 -rwxr-xr-x 1 sagon unige 3703594 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so -> libvtkCommonTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 -> libvtkCommonTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1499456 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so -> libvtkDICOMParser.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 -> libvtkDICOMParser.so.5.6.0 -rwxr-xr-x 1 sagon unige 145360 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so -> libvtkexoIIc.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 -> libvtkexoIIc.so.5.6.0 -rwxr-xr-x 1 sagon unige 312372 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so -> libvtkFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 -> libvtkFiltering.so.5.6.0 -rwxr-xr-x 1 sagon unige 4502701 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so -> libvtkFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 -> libvtkFilteringTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 2185191 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 19 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so -> libvtkftgl.so.5.6.0 lrwxrwxrwx 1 sagon unige 19 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 -> libvtkftgl.so.5.6.0 -rwxr-xr-x 1 sagon unige 60005 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6.0 lrwxrwxrwx 1 sagon unige 31 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so -> libvtkGenericFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 31 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 -> libvtkGenericFiltering.so.5.6.0 -rwxr-xr-x 1 sagon unige 294583 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 34 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so -> libvtkGenericFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 34 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 -> libvtkGenericFilteringTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 153307 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 23 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so -> libvtkGraphics.so.5.6.0 lrwxrwxrwx 1 sagon unige 23 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 -> libvtkGraphics.so.5.6.0 -rwxr-xr-x 1 sagon unige 8696621 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so -> libvtkGraphicsTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 -> libvtkGraphicsTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 2517761 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so -> libvtkHybrid.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 -> libvtkHybrid.so.5.6.0 -rwxr-xr-x 1 sagon unige 3436930 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so -> libvtkHybridTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 -> libvtkHybridTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1085658 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so -> libvtkImaging.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 -> libvtkImaging.so.5.6.0 -rwxr-xr-x 1 sagon unige 4169350 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so -> libvtkImagingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 -> libvtkImagingTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 883379 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 17 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so -> libvtkIO.so.5.6.0 lrwxrwxrwx 1 sagon unige 17 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 -> libvtkIO.so.5.6.0 -rwxr-xr-x 1 sagon unige 6095744 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so -> libvtkIOTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 -> libvtkIOTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1268771 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so -> libvtklibxml2.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 -> libvtklibxml2.so.5.6.0 -rwxr-xr-x 1 sagon unige 1769914 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so -> libvtkmetaio.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 -> libvtkmetaio.so.5.6.0 -rwxr-xr-x 1 sagon unige 643391 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so -> libvtkNetCDF.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 -> libvtkNetCDF.so.5.6.0 -rwxr-xr-x 1 sagon unige 257185 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so -> libvtkpng.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 -> libvtkpng.so.5.6.0 -rwxr-xr-x 1 sagon unige 168598 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so -> libvtkproj4.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 -> libvtkproj4.so.5.6.0 -rwxr-xr-x 1 sagon unige 335939 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so -> libvtkRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 -> libvtkRendering.so.5.6.0 -rwxr-xr-x 1 sagon unige 6120907 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so -> libvtkRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 -> libvtkRenderingTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 2278760 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so -> libvtksqlite.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 -> libvtksqlite.so.5.6.0 -rwxr-xr-x 1 sagon unige 709297 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so -> libvtksys.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 -> libvtksys.so.5.6.0 -rwxr-xr-x 1 sagon unige 305372 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -> libvtkverdict.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0 lrwxrwxrwx 1 sagon unige 30 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so -> libvtkVolumeRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 30 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 -> libvtkVolumeRendering.so.5.6.0 -rwxr-xr-x 1 sagon unige 4500213 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 33 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so -> libvtkVolumeRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 33 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 -> libvtkVolumeRenderingTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 420713 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so -> libvtkWidgets.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 -> libvtkWidgets.so.5.6.0 -rwxr-xr-x 1 sagon unige 2425484 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so -> libvtkWidgetsTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 -> libvtkWidgetsTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1227320 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 89056 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so -rwxr-xr-x 1 sagon unige 89056 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 -rwxr-xr-x 1 sagon unige 89056 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6.0 2017-09-19 20:10 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu>: > 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.gschw...@gmail.com< > mailto:markus.gschw...@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 <ahoo...@mgh.harvard.edu<mailto: > ahoo...@mgh.harvard.edu>>: > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup the shared objects > mv libvtkverdict.so libvtkverdict.so.bk > mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk > # link them to 5.6 > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6 > > then do you get the same error from freeview? > > -Andrew > > On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschw...@gmail.com< > mailto:markus.gschw...@gmail.com>> wrote: > > Dear Andrew, > > The command gives this result: > > [gschwind@login1 ~]$ /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 <ahoo...@mgh.harvard.edu<mailto: > ahoo...@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/:/ /' <<< $LD_LIBRARY_PATH) | grep > libvtkverdict.so > > best, > Andrew > > On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschw...@gmail.com< > mailto:markus.gschw...@gmail.com>> wrote: > > Hi experts, > > I am installing freeusrfer on our cluster which is running Centos6. > > [gschwind@login1 ~]$ 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
