I downloaded some packages for tcl and tk, but they didn't have any effect. I also get this error, which I forgot to include: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 221 vtkKWQdecApp (0x881c1f0): Script: FsgdfPlot_IsWindowShowing 0 Returned Error on line 1: invalid command name "FsgdfPlot_IsWindowShowing" Stack trace: invalid command name "FsgdfPlot_IsWindowShowing" while executing "FsgdfPlot_IsWindowShowing 0"
The output of the command is shown below: $ ldd $FREESURFER_HOME/bin/qdec.bin
linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0xf7ef2000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0xf7e31000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7dc2000) libGL.so.1 => /usr/lib/libGL.so.1 (0xf7d1e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x0050f000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf7d06000) libverdict.so.1.2 => not found libvtkGraphics.so.5.1 => not found libvtkfreetype.so.5.1 => not found libvtkmetaio.so.5.1 => not found libvtkpng.so.5.1 => not found libvtkzlib.so.5.1 => not found libvtkImaging.so.5.1 => not found libvtkFiltering.so.5.1 => not found libvtkCommon.so.5.1 => not found libvtksys.so.5.1 => not found libvtkexoIIc.so.5.1 => not found libvtkNetCDF.so.5.1 => not found libvtkVolumeRendering.so.5.1 => not found libvtkRendering.so.5.1 => not found libvtkftgl.so.5.1 => not found libvtkWidgets.so.5.1 => not found libvtkHybrid.so.5.1 => not found libvtkIO.so.5.1 => not found libvtkDICOMParser.so.5.1 => not found libvtkVolumeRenderingTCL.so.5.1 => not found libvtkRenderingTCL.so.5.1 => not found libvtkFilteringTCL.so.5.1 => not found libvtkWidgetsTCL.so.5.1 => not found libvtkHybridTCL.so.5.1 => not found libvtkGraphicsTCL.so.5.1 => not found libvtkImagingTCL.so.5.1 => not found libvtkIOTCL.so.5.1 => not found libvtkCommonTCL.so.5.1 => not found libKWWidgets.so => not found libz.so.1 => /lib/libz.so.1 (0x001fd000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00bcd000) libdl.so.2 => /lib/libdl.so.2 (0x00bb7000) libpthread.so.0 => /lib/libpthread.so.0 (0xf7ce7000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xf7c2e000) libm.so.6 => /lib/libm.so.6 (0xf7c04000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00df2000) libc.so.6 => /lib/libc.so.6 (0x00a5c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x008e9000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf70ee000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf70eb000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0089a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0050b000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0060d000) libXt.so.6 => /usr/lib/libXt.so.6 (0x00632000) /lib/ld-linux.so.2 (0x00a3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00d4c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d6f000) libSM.so.6 => /usr/lib/libSM.so.6 (0xf70e1000) libICE.so.6 => /usr/lib/libICE.so.6 (0xf70c7000)
Thanks. -Ryan McGarry
Ryan,
I forgot to mention, prior to running the ldd command, type this:
source $FREESURFER_HOME/bin/tcl_setup source $FREESURFER_HOME/bin/vtk_setup source $FREESURFER_HOME/bin/kww_setup
Also, it should not be necessary to download a tcl/tk package, as the tcl/tk package included with freesurfer should work. Worst case is the necessity to build tcl, vtk and kwwidgets from scratch on your system. I'm hoping that is not necessary, but I'm guessing it will be.
Nick
On Fri, 2008-02-08 at 14:24 -0500, William R Mcgarry wrote:
I downloaded some packages for tcl and tk, but they didn't have any effect. I also get this error, which I forgot to include: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 221 vtkKWQdecApp (0x881c1f0): Script: FsgdfPlot_IsWindowShowing 0 Returned Error on line 1: invalid command name "FsgdfPlot_IsWindowShowing" Stack trace: invalid command name "FsgdfPlot_IsWindowShowing" while executing "FsgdfPlot_IsWindowShowing 0"
The output of the command is shown below: $ ldd $FREESURFER_HOME/bin/qdec.bin
linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0xf7ef2000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0xf7e31000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7dc2000) libGL.so.1 => /usr/lib/libGL.so.1 (0xf7d1e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x0050f000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf7d06000) libverdict.so.1.2 => not found libvtkGraphics.so.5.1 => not found libvtkfreetype.so.5.1 => not found libvtkmetaio.so.5.1 => not found libvtkpng.so.5.1 => not found libvtkzlib.so.5.1 => not found libvtkImaging.so.5.1 => not found libvtkFiltering.so.5.1 => not found libvtkCommon.so.5.1 => not found libvtksys.so.5.1 => not found libvtkexoIIc.so.5.1 => not found libvtkNetCDF.so.5.1 => not found libvtkVolumeRendering.so.5.1 => not found libvtkRendering.so.5.1 => not found libvtkftgl.so.5.1 => not found libvtkWidgets.so.5.1 => not found libvtkHybrid.so.5.1 => not found libvtkIO.so.5.1 => not found libvtkDICOMParser.so.5.1 => not found libvtkVolumeRenderingTCL.so.5.1 => not found libvtkRenderingTCL.so.5.1 => not found libvtkFilteringTCL.so.5.1 => not found libvtkWidgetsTCL.so.5.1 => not found libvtkHybridTCL.so.5.1 => not found libvtkGraphicsTCL.so.5.1 => not found libvtkImagingTCL.so.5.1 => not found libvtkIOTCL.so.5.1 => not found libvtkCommonTCL.so.5.1 => not found libKWWidgets.so => not found libz.so.1 => /lib/libz.so.1 (0x001fd000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00bcd000) libdl.so.2 => /lib/libdl.so.2 (0x00bb7000) libpthread.so.0 => /lib/libpthread.so.0 (0xf7ce7000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xf7c2e000) libm.so.6 => /lib/libm.so.6 (0xf7c04000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00df2000) libc.so.6 => /lib/libc.so.6 (0x00a5c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x008e9000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf70ee000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf70eb000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0089a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0050b000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0060d000) libXt.so.6 => /usr/lib/libXt.so.6 (0x00632000) /lib/ld-linux.so.2 (0x00a3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00d4c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d6f000) libSM.so.6 => /usr/lib/libSM.so.6 (0xf70e1000) libICE.so.6 => /usr/lib/libICE.so.6 (0xf70c7000)Thanks. -Ryan McGarry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[pang@localhost qdec]$ source FREESURFER_HOME/bin/tcl_setup bash: /usr/local/freesurfer/bin/tcl_setup: line 48: syntax error near unexpected token `setenv' bash: /usr/local/freesurfer/bin/tcl_setup: line 48: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3' [pang@localhost qdec]$ source $FREESURFER_HOME/bin/vtk_setup bash: /usr/local/freesurfer/bin/vtk_setup: line 80: syntax error: unexpected end of file [pang@localhost qdec]$ source $FREESURFER_HOME/bin/kww_setup bash: /usr/local/freesurfer/bin/kww_setup: line 62: syntax error: unexpected end of file [pang@localhost qdec]$ ldd $FREESURFER_HOME/bin/qdec.bin linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0xf7ef2000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0xf7e31000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7dc2000) libGL.so.1 => /usr/lib/libGL.so.1 (0xf7d1e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x0050f000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf7d06000) libverdict.so.1.2 => not found libvtkGraphics.so.5.1 => not found libvtkfreetype.so.5.1 => not found libvtkmetaio.so.5.1 => not found libvtkpng.so.5.1 => not found libvtkzlib.so.5.1 => not found libvtkImaging.so.5.1 => not found libvtkFiltering.so.5.1 => not found libvtkCommon.so.5.1 => not found libvtksys.so.5.1 => not found libvtkexoIIc.so.5.1 => not found libvtkNetCDF.so.5.1 => not found libvtkVolumeRendering.so.5.1 => not found libvtkRendering.so.5.1 => not found libvtkftgl.so.5.1 => not found libvtkWidgets.so.5.1 => not found libvtkHybrid.so.5.1 => not found libvtkIO.so.5.1 => not found libvtkDICOMParser.so.5.1 => not found libvtkVolumeRenderingTCL.so.5.1 => not found libvtkRenderingTCL.so.5.1 => not found libvtkFilteringTCL.so.5.1 => not found libvtkWidgetsTCL.so.5.1 => not found libvtkHybridTCL.so.5.1 => not found libvtkGraphicsTCL.so.5.1 => not found libvtkImagingTCL.so.5.1 => not found libvtkIOTCL.so.5.1 => not found libvtkCommonTCL.so.5.1 => not found libKWWidgets.so => not found libz.so.1 => /lib/libz.so.1 (0x001fd000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00bcd000) libdl.so.2 => /lib/libdl.so.2 (0x00bb7000) libpthread.so.0 => /lib/libpthread.so.0 (0xf7ce7000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xf7c2e000) libm.so.6 => /lib/libm.so.6 (0xf7c04000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00df2000) libc.so.6 => /lib/libc.so.6 (0x00a5c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x008e9000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf70ee000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf70eb000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0089a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0050b000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0060d000) libXt.so.6 => /usr/lib/libXt.so.6 (0x00632000) /lib/ld-linux.so.2 (0x00a3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00d4c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d6f000) libSM.so.6 => /usr/lib/libSM.so.6 (0xf70e1000) libICE.so.6 => /usr/lib/libICE.so.6 (0xf70c7000)
Ryan,
It appears that tcsh is not being used. Enter tcsh by typing:
tcsh
then initialize freesurfer by typing:
source $FREESURFER_HOME/SetUpFreeSurfer.csh
then try the qdec utility again (and if still gives the same problems, then run the ldd command and send me the results).
You can also just type:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
if your using bash.
Nick
On Fri, 2008-02-08 at 14:33 -0500, William R Mcgarry wrote:
[pang@localhost qdec]$ source FREESURFER_HOME/bin/tcl_setup bash: /usr/local/freesurfer/bin/tcl_setup: line 48: syntax error near unexpected token `setenv' bash: /usr/local/freesurfer/bin/tcl_setup: line 48: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3' [pang@localhost qdec]$ source $FREESURFER_HOME/bin/vtk_setup bash: /usr/local/freesurfer/bin/vtk_setup: line 80: syntax error: unexpected end of file [pang@localhost qdec]$ source $FREESURFER_HOME/bin/kww_setup bash: /usr/local/freesurfer/bin/kww_setup: line 62: syntax error: unexpected end of file [pang@localhost qdec]$ ldd $FREESURFER_HOME/bin/qdec.bin linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0xf7ef2000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0xf7e31000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7dc2000) libGL.so.1 => /usr/lib/libGL.so.1 (0xf7d1e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x0050f000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf7d06000) libverdict.so.1.2 => not found libvtkGraphics.so.5.1 => not found libvtkfreetype.so.5.1 => not found libvtkmetaio.so.5.1 => not found libvtkpng.so.5.1 => not found libvtkzlib.so.5.1 => not found libvtkImaging.so.5.1 => not found libvtkFiltering.so.5.1 => not found libvtkCommon.so.5.1 => not found libvtksys.so.5.1 => not found libvtkexoIIc.so.5.1 => not found libvtkNetCDF.so.5.1 => not found libvtkVolumeRendering.so.5.1 => not found libvtkRendering.so.5.1 => not found libvtkftgl.so.5.1 => not found libvtkWidgets.so.5.1 => not found libvtkHybrid.so.5.1 => not found libvtkIO.so.5.1 => not found libvtkDICOMParser.so.5.1 => not found libvtkVolumeRenderingTCL.so.5.1 => not found libvtkRenderingTCL.so.5.1 => not found libvtkFilteringTCL.so.5.1 => not found libvtkWidgetsTCL.so.5.1 => not found libvtkHybridTCL.so.5.1 => not found libvtkGraphicsTCL.so.5.1 => not found libvtkImagingTCL.so.5.1 => not found libvtkIOTCL.so.5.1 => not found libvtkCommonTCL.so.5.1 => not found libKWWidgets.so => not found libz.so.1 => /lib/libz.so.1 (0x001fd000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00bcd000) libdl.so.2 => /lib/libdl.so.2 (0x00bb7000) libpthread.so.0 => /lib/libpthread.so.0 (0xf7ce7000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xf7c2e000) libm.so.6 => /lib/libm.so.6 (0xf7c04000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00df2000) libc.so.6 => /lib/libc.so.6 (0x00a5c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x008e9000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf70ee000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf70eb000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0089a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0050b000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0060d000) libXt.so.6 => /usr/lib/libXt.so.6 (0x00632000) /lib/ld-linux.so.2 (0x00a3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00d4c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d6f000) libSM.so.6 => /usr/lib/libSM.so.6 (0xf70e1000) libICE.so.6 => /usr/lib/libICE.so.6 (0xf70c7000)
[pang@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-rh9-stable-pub-v4.0.2 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/freesurfer/fsl [pang@localhost ~]$ source FREESURFER_HOME/bin/tcl_setup bash: FREESURFER_HOME/bin/tcl_setup: No such file or directory [pang@localhost ~]$ source $FREESURFER_HOME/bin/vtk_setup bash: /usr/local/freesurfer/bin/vtk_setup: line 80: syntax error: unexpected end of file [pang@localhost ~]$ source $FREESURFER_HOME/bin/kww_setup bash: /usr/local/freesurfer/bin/kww_setup: line 62: syntax error: unexpected end of file [pang@localhost ~]$ ldd $FREESURFER_HOME/bin/qdec.bin linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0xf7ef2000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0xf7e31000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xf7dc2000) libGL.so.1 => /usr/lib/libGL.so.1 (0xf7d1e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x0050f000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xf7d06000) libverdict.so.1.2 => not found libvtkGraphics.so.5.1 => not found libvtkfreetype.so.5.1 => not found libvtkmetaio.so.5.1 => not found libvtkpng.so.5.1 => not found libvtkzlib.so.5.1 => not found libvtkImaging.so.5.1 => not found libvtkFiltering.so.5.1 => not found libvtkCommon.so.5.1 => not found libvtksys.so.5.1 => not found libvtkexoIIc.so.5.1 => not found libvtkNetCDF.so.5.1 => not found libvtkVolumeRendering.so.5.1 => not found libvtkRendering.so.5.1 => not found libvtkftgl.so.5.1 => not found libvtkWidgets.so.5.1 => not found libvtkHybrid.so.5.1 => not found libvtkIO.so.5.1 => not found libvtkDICOMParser.so.5.1 => not found libvtkVolumeRenderingTCL.so.5.1 => not found libvtkRenderingTCL.so.5.1 => not found libvtkFilteringTCL.so.5.1 => not found libvtkWidgetsTCL.so.5.1 => not found libvtkHybridTCL.so.5.1 => not found libvtkGraphicsTCL.so.5.1 => not found libvtkImagingTCL.so.5.1 => not found libvtkIOTCL.so.5.1 => not found libvtkCommonTCL.so.5.1 => not found libKWWidgets.so => not found libz.so.1 => /lib/libz.so.1 (0x001fd000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00bcd000) libdl.so.2 => /lib/libdl.so.2 (0x00bb7000) libpthread.so.0 => /lib/libpthread.so.0 (0xf7ce7000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xf7c2e000) libm.so.6 => /lib/libm.so.6 (0xf7c04000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00df2000) libc.so.6 => /lib/libc.so.6 (0x00a5c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x008e9000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xf70ee000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xf70eb000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0089a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x0050b000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x0060d000) libXt.so.6 => /usr/lib/libXt.so.6 (0x00632000) /lib/ld-linux.so.2 (0x00a3d000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00d4c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00d6f000) libSM.so.6 => /usr/lib/libSM.so.6 (0xf70e1000) libICE.so.6 => /usr/lib/libICE.so.6 (0xf70c7000)
freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
William R Mcgarry