BrainVISA 4.3 + Mac OSX 10.6.8

Questions about BrainVisa usage and installation

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mtrsteve
Posts: 2
Joined: Mon Sep 24, 2012 7:44 pm

BrainVISA 4.3 + Mac OSX 10.6.8

Post by mtrsteve »

Hello, I am trying to install BrainVISA on my mac, and am having some difficulties.

I started with the binary installer, which worked for anatomist, but not for BrainVISA if I try launching form terminal, I get an error that I am missing a Qt library (QtDBus). If I try to install from the source, following the instructions, I get to the configure step, and hit the following error:

/tmp/brainvisa-cmake/bin/bv_maker configure
Traceback (most recent call last):
File "/tmp/brainvisa-cmake/bin/bv_maker", line 719, in <module>
f()
File "/tmp/brainvisa-cmake/bin/bv_maker", line 259, in __call__
o.configure()
File "/tmp/brainvisa-cmake/bin/bv_maker", line 551, in configure
os.stat( directory ) # Raise appropriate error if directory does not exist
OSError: [Errno 2] No such file or directory: '/Users/tynanstevens/brainvisa/source/opensource/optical_imaging/optical_imaging-gpl/trunk'

I have tried this with the trunk, latest_release, and bug_fix versions with the same error. I tried downloading the .../optical_imaging... source for version 4.2.1, in which case I get an error at the build step instead. I can reproduce these errors if needed and provide more console output.

-Tynan
mtrsteve
Posts: 2
Joined: Mon Sep 24, 2012 7:44 pm

Re: BrainVISA 4.3 + Mac OSX 10.6.8

Post by mtrsteve »

I should mention that version 4.2.1 installs and launches successfully.
I am new to BrainVISA, so I thought I would get the newest version, but I will use 4.2.1 for now. Nonetheless, there is clearly something missing from both the binary and source distros for version 4.3
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riviere
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Re: BrainVISA 4.3 + Mac OSX 10.6.8

Post by riviere »

Well, I didn't think QtDBus was actually used or needed, and I don't see it in binary packages 4.2.1 either, so I suspect the problem is not completely due to QtDBus.
Have you looked at http://brainvisa.info/forum/viewtopic.php?f=2&t=1561 and http://brainvisa.info/forum/viewtopic.php?f=2&t=1476 ?

For the problems with the sources, there is actually a bug in the projects list, optical_imaging is not an official, released project, so should not be part of the list. We will remove it. For other build problems, I would rather try to make the binary packages work first, because compiling on Mac requires to compile and install also some dependency libraries, and thus is not a little work.

Denis
alexsavio
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Joined: Tue Nov 13, 2012 5:33 pm

Re: BrainVISA 4.3 + Mac OSX 10.6.8

Post by alexsavio »

Hi,

Something similar is happening to me in Ubuntu 12.10 amd64:

$./bv_maker configure
Traceback (most recent call last):
File "./bv_maker", line 719, in <module>
f()
File "./bv_maker", line 259, in __call__
o.configure()
File "./bv_maker", line 551, in configure
os.stat( directory ) # Raise appropriate error if directory does not exist
OSError: [Errno 2] No such file or directory: '/home/alexandre/Software/brainvisa/source/connectomist/old_connectomist-private/tags/4.3.0'

Here is the content of my ~/.brainvisa/bv_maker.cfg:
[ source $HOME/Software/brainvisa/source ]
+ standard latest_release

[ build $HOME/Software/brainvisa/build ]
build_type = Release
make_options = -j8
standard latest_release $HOME/Software/brainvisa/source

I'm interested in compiling brainvisa in order to have the anatomist python modules available from my python installation.

Thanks for your help.

Cheers,
Alex
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riviere
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Re: BrainVISA 4.3 + Mac OSX 10.6.8

Post by riviere »

Hi Alex,
Well, there are some parts which are not open-source (at least for now), so if you are not a collaborator owning an account in the svn repository, you should only use the opensource part: replace "standard" with "opensource" in your bv_maker.cfg file. You will be able to get and build Axon (the "brainvisa" program), Aims, Anatomist, but not all of the advanced processing tools, sorry.
The binary version, on the contrary, includes all the tools, even the closed-source ones, which are free to use in a non-commercial research context.
Why do you have to build, does the binary version not work for you ?
Denis
alexsavio
Posts: 2
Joined: Tue Nov 13, 2012 5:33 pm

Re: BrainVISA 4.3 + Mac OSX 10.6.8

Post by alexsavio »

Hi Denis,

Thank you for your reply.

I just wanted to build it so I could have access to anatomist from Python.
I would like to keep using my iPython and python 2.7, so I tried this:

import sys
sys.path.append('/home/alexandre/Software/brainvisa-4.3.0/python/')
import anatomist.direct.api as anatomist

But I get an error: libpython2.5.so.1.0: cannot open shared object file.
Is there any way around this without adding "/home/alexandre/Software/brainvisa-4.3.0/lib" to my "ld_library_path" in my system? Can I do it from python?

I'm downloading and checking if the api to anatomist is included in the opensource branch.

My kind regards,
Alex
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riviere
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Re: BrainVISA 4.3 + Mac OSX 10.6.8

Post by riviere »

Hi Alex,
OK I see. If you want to use your system python (2.7) then you will really need to recompile since we have some compiled modules (for the bindings with C++ libs) which are linked against python 2.5.
You can use the python/ipython from the binary distribution (you can setup the environments variables using the bv_env.sh script in the bin/ directory), but it will not be your system python 2.7.
If it is for anatomist/pyanatomist, you can build from the opensource parts.
Denis
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