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bv freesurfer toolbox
Posted: Thu Sep 18, 2014 8:41 am
by SylvainT
Hi!
I'm trying to use the freesurfer toolbox... (I think I havn't used it since the BV 4.4 upgrade)
My BrainVISA is installed and functional, my freesurfer as well, but when I try to use one of the bricks of the freesurfer toolbox (and actually, some bricks, like the "Freesurfer / BrainVISA full pipeline", are greyd out), I get the following error:
mri_convert: /opt/brainvisa/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert)
I read this as if the freesurfer binaries cannot be run from the BrainVISA environment, but I'm not sure... Is that it? Anything I can do?
Cheers,
Sylvain
ps: I'm using brainvisa-Mandriva-2008.0-x86_64-4.4.0-2013_11_18.tar.bz2 and freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on a debian system...
Re: bv freesurfer toolbox
Posted: Thu Sep 18, 2014 5:50 pm
by riviere
Hi Sylvain,
Normally programs which are external to BrainVisa (located outside the BV main directory) should be called with BV environment cleared: paths and other environment variables are reset to their initial value, so it should work smoothly. But obviously, here it does not...
I don't have an explanation for this right now.
Have you sourced the bv_env.sh script in your shell (or .bashrc or something) or run brainvisa from its bin/ directory ? (it should work in both cases but it might help me to find out the cause of the problem)
Have you setup FreeSurfer config in the preferences ? Does your FreeSurfer installation contain an environment script, FreeSurferEnv.sh ?
You can try moving out the libstdc++ library from brainvisa, like in
this post but I cannot be sure it will solve all problems.
Denis
Re: bv freesurfer toolbox
Posted: Thu Sep 18, 2014 5:59 pm
by riviere
Oh maybe I have a beginning of idea. I wonder if env variables which do not have a value at the beginning are actually reset when running external commands from Brainvisa.
- Before running BV or sourcing its bv_env.sh script, do you have a non-empty LD_LIBRARY_PATH env variable ?
- or, when running /opt/brainvisa/bin/bv_env (with no arguments), do you have a line with "BRAINVISA_UNENV_LD_LIBRARY_PATH" ?
If not, this may be the problem, and it's a bug in our code.
Then you can try tricking it by actually settting something in the variable (even non relevant):
Code: Select all
export LD_LIBRARY_PATH=/budubudu
/opt/brainvisa/bin/brainvisa
Denis
Re: bv freesurfer toolbox
Posted: Tue Sep 23, 2014 9:59 am
by SylvainT
thanks Denis!
(I've already tried a few things without success, but I need to look at this in more details, I will keep you posted...)
Re: bv freesurfer toolbox
Posted: Fri Nov 14, 2014 7:35 pm
by SylvainT
Hi Denis,
Back to this
First, here is an extra piece of info: the error I'm gettingactually pops out at the time I launch BV:
Code: Select all
Loading toolbox brainrat
Loading toolbox connectomist
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox editors
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
light mode
The log file for this session is '/home/takerkart/.brainvisa/brainvisa.log'
mri_convert: /riou/work/scalp/tools/brainvisa-4.4.0/lib/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found (required by mri_convert)
/usr/share/fsl/data: parse directories and insert items
/usr/share/fsl/data: 4 files are stored as 4 DiskItems in 0 seconds
Then, here is some feedback on your suggestions:
riviere wrote:Oh maybe I have a beginning of idea. I wonder if env variables which do not have a value at the beginning are actually reset when running external commands from Brainvisa.
- Before running BV or sourcing its bv_env.sh script, do you have a non-empty LD_LIBRARY_PATH env variable ?
nope, my LD_LIBRARY_PATH is empty before launching BV...
riviere wrote:
- or, when running /opt/brainvisa/bin/bv_env (with no arguments), do you have a line with "BRAINVISA_UNENV_LD_LIBRARY_PATH" ?
If not, this may be the problem, and it's a bug in our code.
that line is empty when I run /opt/brainvisa/bin/bv_env:
Code: Select all
export BRAINVISA_UNENV_LD_LIBRARY_PATH=''
riviere wrote:
You can try moving out the libstdc++ library from brainvisa, like in
this post but I cannot be sure it will solve all problems.
This actually does the job!
So I don't know if all this gives you more information about what the problem is, but at least I have a temporary way to do what I need to do
Let me know if you want me to test something else to help you diagnose the problem...
Cheers,
Sylvain