install on Ubuntu 16.04.2 LTS

Questions about BrainVisa usage and installation

Moderators: denghien, riviere

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

install on Ubuntu 16.04.2 LTS

Post by joost »

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

Post by joost »

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

Post by joost »

Some further specs of my machine.
merci
Attachments
mySpecs.txt
(45.98 KiB) Downloaded 384 times
joost
Posts: 86
Joined: Tue Feb 05, 2008 1:56 pm

Re: install on Ubuntu 16.04.2 LTS

Post by joost »

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'
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Re: install on Ubuntu 16.04.2 LTS

Post by riviere »

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
Post Reply