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...
bv freesurfer toolbox
- riviere
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- Posts: 1361
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Re: bv freesurfer toolbox
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
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
- riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: bv freesurfer toolbox
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):
Denis
- 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
Re: bv freesurfer toolbox
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...)
(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
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:
Then, here is some feedback on your suggestions:
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
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
nope, my LD_LIBRARY_PATH is empty before launching BV...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 ?
that line is empty when I run /opt/brainvisa/bin/bv_env: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.
Code: Select all
export BRAINVISA_UNENV_LD_LIBRARY_PATH=''
This actually does the job!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.
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