install on Ubuntu 16.04.2 LTS

Questions about BrainVisa usage and installation

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joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

install on Ubuntu 16.04.2 LTS

Postby joost » Thu Mar 02, 2017 3:40 pm

Hi,

I'm trying to get brainvisa working on Ubuntu Xenial. in my .bashrc i have:
function brainvisa_setup
{
. /opt/brainvisa/bin/bv_env.sh /opt/brainvisa
}

when i start brainvisa the update database window frame opens, but then hangs. i see no python rubbing in my 'top'. this is the on screen output:

Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 72: non-double matrix element
Fontconfig error: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 72: non-double matrix element
Fontconfig warning: "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf", line 80: saw unknown, expected number
Fontconfig warning: "/etc/fonts/conf.d/11-lcdfilter-default.conf", line 14: invalid constant used : lcddefault
Loading toolbox brainrat
Loading toolbox connectomist
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
The log file for this session is '/home/jjanssen/.brainvisa/brainvisa10.log'
Database /opt/brainvisa/share/brainvisa-share-4.5 must be updated because the
database file is too old.
/opt/brainvisa/brainvisa/toolboxes/cortical_surface/processes/functional/misc/projAverageVolumes.py: inconsistent use of tabs and spaces in indentation
/opt/brainvisa/brainvisa/toolboxes/morphologist/processes/Sulci/Recognition/recognition_error.py: inconsistent use of tabs and spaces in indentation
/usr/share/fsl/5.0/data: parse directories and insert items
/usr/share/fsl/5.0/data: 4 files are stored as 4 DiskItems in 0 seconds
ICE default IO error handler doing an exit(), pid = 7037, errno = 32

my python version is 2.7.3 (for what its worth)
any pointers?
merci

joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: install on Ubuntu 16.04.2 LTS

Postby joost » Thu Mar 02, 2017 3:45 pm

just adding: i am using Linux 64 bits (glibc 2.6) (built on Mandriva 2008)
merci

joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: install on Ubuntu 16.04.2 LTS

Postby joost » Thu Mar 02, 2017 5:28 pm

Some further specs of my machine.
merci
Attachments
mySpecs.txt
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joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: install on Ubuntu 16.04.2 LTS

Postby joost » Fri Mar 03, 2017 10:51 am

if i type Qt at the command line I get:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
ImportError: No module named 'encodings'

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riviere
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Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: install on Ubuntu 16.04.2 LTS

Postby riviere » Fri Mar 03, 2017 2:22 pm

Hi,

When I run the linux64-glibc2.6 version on my Ubuntu 16.04 machine, I get the Fontconfig error messages, but it seems to run normally anyway. I can update databases. I don't know if you could try moving away the libfontconfig.so.* files from the lib/ directyory of bainvisa, just to see if the system one would work (it may not) and if yes if it is the cause of the problem, but I don't see why I don't have the same behavior.
So I don't have an answer for your problem...

if i type Qt at the command line I get:

Qt? Qt is not a command ?

Once you have run your brainvisa_setup function in a terminal, that terminal will probably make a bunch of system commands unusable since it sets PATHs to libraries from the BV distrib (those from Mandriva 2008) and will likely be incompatible with your system commands.

Denis


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