normalization with fsl within morphologist

[SylvainT]

Hi all, I'm trying to use the FSL normalization within morphologist... (having to process a lot of subjects, I want to avoid clicking on AC / PC every time)

I'm on debian squeeze with BV 4.1.1, and the neurodebian version of fsl (the one with all executables starting with the fsl-4.1 prefix)... I get some library incompatibility errors, for example:

/usr/share/fsl/4.1/bin/flirt: /usr/local/scipkg/brainvisa/brainvisa-Mandriva-2008.0-x86_64-4.1.1-2011_09_13/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/share/fsl/4.1/bin/flirt)

Any hint about what to do?? (I'm guessing recompiling fsl from the sources within the brainvisa environment is a solution, but I don't even want to give this a try coz I'm sure it's going to be a huuuuuuuuuge pain )

Thanks,

Sylvain

[Dominique Geffroy]

Hi Sylvain,

I see, I guess this is just because your Brainvisa package is installed in /usr/local.
Indeed, Brainvisa is supposed to reinitialize system environment variables when starting an external command (that is not in the BV package) like fsl in your case.
But in BV 4.1.1, this is not done if Brainvisa is installed in /usr. We probably should correct this test...
Meanwhile, could you try to move Brainvisa package elsewhere and see if it happens again ?

Dominique

[SylvainT]

Thanks Dominique, moving the BrainVisa installation dir somewhere else makes it work!

And actually, since we always install BrainVisa in the same place (system-wide in /usr/local) on a server for a bunch of users in our lab, we'd seen this kind of problems several times (when launching different applications than Brainvisa in the unix window where BrainVisa was launched from, we often see this kind of messages having to deal with linking with dynamic librairies ), but always got around it by just opening another window to launch other applications...

Cheers,

Sylvain

[riviere]

Hi Sylvain,
We have made a fix for your problem:
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... oConfig.py
You just have to copy the file in the brainvisa/ subdirectory of the BV package.
Denis