brainvisa installation issues

[vincentdore]

Hello,

I am trying to install brainVISA on ubuntu 10.10 64bit.
I download the binary package 4.0.2 for linux 64bits :
when running

Code: Select all

 ./setup.sh

I got some errors as :

/home/vincent/local/brainvisa/bin/commands-links/python: 1: ELF: not found

when changing the python version. I got :

Fatal Python error: Py_Initialize: can't initialize sys standard streams
ImportError: No module named encodings.utf_8

for python 3.1
and :

'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/home/vincent/local/brainvisa/build-configSubInstall.py", line 36, in <module>
import os, sys, string, re, copy, getopt, glob, shutil
ImportError: No module named os

for python 2.6

I also tryed to compile the source code but the same I got some issues, (see attached file) when using

Code: Select all

build-config --version 4.0 --verbose --buildMode release anatomist axon brainvisa-share &>error_source.txt

I got the same issues with different version of brainvisa.
Thanks in advance for anyone that can help me,
Vincent.

[Dominique Geffroy]

Hello,

What do you mean by "changing the python version" ? A suitable version of Python is already included in Brainvisa packages, and Brainvisa uses this version, not a version installed on the system. So, you cannot try different versions of python... I don't really understand what you mean.
Maybe you could try the linux 32 bits package ? It has been built on an older linux system, so maybe it is compatible with more systems.

For the compilation from the source, the error message seems to indicate that you don't have all the needed source files. How did you get the source ?

Dominique

[vincentdore]

Thank you Dominique for your answer,

I changed the python version because of the error given by the included python version :

[: 23: unexpected operator
/home/vincent/local/brainvisa/bin/commands-links/python: 1: ELF: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 3: ����: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 3: ���: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 5: �: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 5: �
@��@�
�@�����: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 7: �
�@�: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 7: �@�
�@libpython2.5.so.1.0__gmon_start___Jv_RegisterClassesPy_Mainlibpthread.so.0libdl.so.2libutil.so.1libm.so.6libc.so.6__libc_start_main_edata__bss_start_end__libc_csu_fini_IO_stdin_used__data_start__libc_csu_initGLIBC_2.2.5rui: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 9: �: not found
/home/vincent/local/brainvisa/bin/commands-links/python: 9: �: not found

The 32bits works fine!
Thanks,
Vincent

[Sylvain]

Hello there,

we just recently move to Brainvisa 4.0.2 from 3.2 and we're having issues accessing our existing database after this update. When I start brainvisa, I see a warning saying the database is from an older version (3.0). Then I run the Convert Old Database process, which goes all fine, except that in the terminal, I see the following warning:

WARNING: internal error: an sqlite connection on u'/MEG_data/MRI_database/database-2.0.sqlite' is opened for thread MainThread but the corresponding ThreadSafeSQLiteConnection instance (number 1) is beign deleted in thread Thread-1. Method currentThreadCleanup() should have been called from MainThread to supress this warning.

I did not select the 'Clean Database' option from the process as I was not sure whether this would actually delete data files or not.

This all results in not being able to launch the segmentation pipeline or any other process because the data list from our database now is empty (although fortunately, all data files are present).

Please advise,

[riviere]

Hi Sylvain,

- did the "update database" improve anything at all ?
- How are the files organized after conversion ? Is it:

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<protocol>/<subject>/t1mri/<acquisition ("default_acquisition")>/<subject>.nii
<protocol>/<subject>/t1mri/<acquisition>/<analysis ("default_analysis")>/[segmentation images]

- if yes, in the database settings, is its ontology correctly set to "brainvisa-3.1.0", or is is still "brainvisa-3.0" ? (to see it, edit the properties of your database, and see in "expert_settings")

The database conversion normally does not erase files, but moves some unneeded files in the Trash subdir of the database.

Denis

[Sylvain]

Thank you so much, Denis!

I changed the ontology to 3.1 and it worked like a charm!

thanks again!