Hi JungSun,

Could you check if the problem occur with the nightly version ?

The nightly version can be downloaded from http://download.slicer.org

Thanks for your help,
Jc

Hi,

I am sorry that the problem is not solved in Nightly version-2015-09-21.

Thank you

Thanks for checking.

To summarize, here are the steps to reproduce the crash:

• downloading Slicer nightly using for example: wget --content-disposition http://download.slicer.org/bitstream/436389
• extracting the archive using: tar -xzvf Slicer-4.4.0-2015-09-23-linux-amd64.tar.gz
• running Slicer using: ./Slicer
• Open "DWIConverted"
• click on the "..." on the right of the "FSL Nifti file" input
• => Crash

After confirming you followed these steps, would it be possible for you to copy the output of the following command:

./Slicer --launch /usr/bin/ldd ./bin/SlicerApp-real

Could you also attach to this issue the file: ~/.config/Trolltech.conf

When you saved a copy of "~/.config/Trolltech.conf", try to delete the file and see if the crash still happen.

Thank you for your kind advice.

But it does not work.

I installled new Slicer as your instruction.

But new version shows an error during loading modules (please see: cap_error_before.png)
As you can see, DWIconvert module is not loaded, so I cannot test it.

After delete Trolltech.conf, I run new version of Slicer.
Then it shows one error during loading modules (see : cap_error_after.png)
When I clicked the '...' in on the right of the FSL NIFTI file input, it shows an error "incompatible QT error"

I attached two ./bin/slicerapp-real (one is before deleting Trolltech, the other is after deleting Trolltech)
and attached Trolltech_before.conf and Trolltech_after.conf

Hi Jae,

Did you make any progress on this particular issue ?

Just to confirm, you also deleted all settings in "~/.config/NA-MIC" folder ?

Hi,

I tested it after I deleted ~/.config/NA-MIC folder and Trolltech.conf and Trolltech folder.

But it shows the same error.

Thanks for testing.

1) What are the value of your current env variables ?

You could get them by typing "export" in a terminal. I am particularly interest about the PATH and LD_LIBRARY_PATH ones.

2) An other things to try would be:

• Start a terminal with the Slicer env:

  ./Slicer --launch /usr/bin/gnome-terminal

• run the following code from the top-level Slicer superbuild folder:

  $ for lib in $(find . | grep ".so$"); do echo ">>> $lib"; ldd ${lib}; done > slicer_all_deps.txt
  $ cat slicer_all_deps.txt | grep "4.8.5" | wc -l
  0
  $ cat slicer_all_deps.txt | grep "4.8.6" | wc -l
  1590

In your case, I would expect the grep for "4.8.6" to return something. Then you could look at the file "slicer_all_deps.txt" to get more details ...

Thanks for your help,

Hth
Jc

Hi,

I am new at linux and image analysis. I am trying to make my computer's setting similar to PNL computer. So there are unnecessary PATH definition and programs.

1. My default shell is TCSH. Here is my path definition.
   /projects/schiz/software/condor/bin:
   /projects/schiz/software/condor/sbin:
   /projects/schiz/software/freesurfer/bin:
   /projects/schiz/software/freesurfer/fsfast/bin:
   /projects/schiz/software/freesurfer/tktools:
   /usr/local/fsl/bin:
   /projects/schiz/software/freesurfer/mni/bin:
   /home/ljs/anaconda/bin:
   /usr/StorMan/pegasus/bin:
   /usr/StorMan/ssl/bin:
   /projects/schiz/software/condor/bin:
   /projects/schiz/software/condor/sbin:
   /projects/schiz/software/freesurfer/bin:
   /projects/schiz/software/freesurfer/fsfast/bin
   /projects/schiz/software/freesurfer/tktools:
   /usr/local/fsl/bin:
   /projects/schiz/software/freesurfer/mni/bin:
   /projects/schiz/software/condor/bin:
   /projects/schiz/software/condor/sbin:
   /projects/schiz/software/freesurfer/bin:
   /projects/schiz/software/freesurfer/fsfast/bin:
   /projects/schiz/software/freesurfer/tktools:
   /usr/local/fsl/bin:
   /projects/schiz/software/freesurfer/mni/bin:
   /usr/lib64/qt-3.3/bin
   :/usr/local/bin:
   /usr/local/sbin:
   /usr/bin:
   /usr/sbin:
   /bin:
   /sbin:/projects/schiz/software/pnlutil:
   /projects/schiz/software/measuretracts:
   /projects/schiz/software/NAMICExternalProjects-build/bin:
   /projects/schiz/software/mricron:
   /projects/schiz/software/Slicer-4.4.0-2015-06-16-linux-amd64/bin:
   /projects/schiz/software/Slicer-4.4.0-2015-06-16-linux-amd64:
   /projects/schiz/software/ENIGMA/scripts:
   /projects/schiz/software/Slicer3-3.6.3-2011-03-04-linux-x86_64/lib/TclTk/lib:/home/ljs/data/image/scripts:
   /projects/schiz/software/mricron_lx:
   /projects/schiz/software/pnlutil/scripts-all:
   /home/ljs/data/image/scripts/ENIGMA/scripts:
   /usr/local/MATLAB/R2012a/bin:
   /projects/schiz/software/pnlutil:
   /projects/schiz/software/measuretracts:
   /projects/schiz/software/NAMICExternalProjects-build/bin:
   /projects/schiz/software/mricron:
   /projects/schiz/software/Slicer-4.4.0-2015-06-16-linux-amd64/bin:
   /projects/schiz/software/Slicer-4.4.0-2015-06-16-linux-amd64:
   /projects/schiz/software/ENIGMA/scripts:
   /projects/schiz/software/Slicer3-3.6.3-2011-03-04-linux-x86_64/lib/TclTk/lib:
   /home/ljs/data/image/scripts:
   /projects/schiz/software/mricron_lx:
   /projects/schiz/software/pnlutil/scripts-all:
   /home/ljs/data/image/scripts/ENIGMA/scripts:
   /usr/local/MATLAB/R2012a/bin:
   /home/ljs/share/Dropbox/research/code:
   /projects/schiz/software/pnlutil:
   /projects/schiz/software/measuretracts:
   /projects/schiz/software/NAMICExternalProjects-build/bin:
   /projects/schiz/software/mricron:
   /projects/schiz/software/Slicer-4.4.0-2015-06-16-linux-amd64/bin:
   /projects/schiz/software/Slicer-4.4.0-2015-06-16-linux-amd64:/projects/schiz/software/ENIGMA/scripts:
   /projects/schiz/software/Slicer3-3.6.3-2011-03-04-linux-x86_64/lib/TclTk/lib:/home/ljs/data/image/scripts:
   /projects/schiz/software/mricron_lx:
   /projects/schiz/software/pnlutil/scripts-all:
   /home/ljs/data/image/scripts/ENIGMA/scripts:
   /usr/local/MATLAB/R2012a/bin:
   /home/ljs/share/Dropbox/research/code

2. I changed the tcsh shell to bash to run your script. And most file in ./lib do not have 'x' permissions. So there are many warnings ('ldd : warning ~~~ ) when I ran your scritps. So I have to change the mode of file in ./lib to 750.
   Then I got the slicer_all_deps.txt file.
   But the number of file with 4.8.6 and 4.8.5 is 0. So I attached file.

Thank you for your help.
If you want to check my computer online or off-line, you can do it.

And there is no definition of LD_LIBRARY_PATH in tcsh.

Hi Jae,

I noticed that you run the command I posted in a regular shell. Make sure to start a terminal with the Slicer environment before running the command.

Two options:

./Slicer --launch /usr/bin/gnome-terminal

or

eval $("/path/to/Slicer" --launcher-show-set-environment-commands)

.

Note that since this issue is most likely due to an environment configuration issue, I am un-targeting the issue.

Hi Jae,

What is the status on this ?

Jc

The problem cannot be resolved without getting further feedback from the reporter.