missing anatomist module after source build

Questions about BrainVisa usage and installation

Moderators: denghien, riviere

Post Reply
atsui
Posts: 13
Joined: Fri Jan 13, 2012 9:23 pm
Location: Davis, CA USA

missing anatomist module after source build

Post by atsui »

Hi,

I built the latest release of BrainVISA (4.3) from source using bv_maker. Next, I go to my build dir and run bv_env to generate environment variables that I source into my bash shell, and then I run brainvisa. The program seems to work, except certain tools are greyed out. Specifically, in Morphologist > Segmentation Pipeline > components, I want to run Prepare Subject for Anatomical Pipeline, but it is greyed out and double-clicking it gives an error:

The process morphologist/processes/segmentationpipeline/components/preparesubject.py is not available: Cannot find anatomist module

There are other tools depending on anatomist module that are similarly disabled. I think anatomist is a core module of BrainVISA, so I wonder what I did wrong in the build? I didn't see any obvious error messages in the configure and build steps.

I could use some advice on how to debug this. I'm working on Ubuntu 13.04, and I've attached my brainvisa.log file for what it's worth. I can provide any other information if needed as well.

Thanks,

--Alex
Attachments
brainvisa.log
(22.79 KiB) Downloaded 277 times
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Re: missing anatomist module after source build

Post by riviere »

Hi Alex,

I don't see any evidently suspicious things in your log.
I have 2 hypotheses: either Anatomist is not correctly compiled, or misses a system library, or the python bindings for anatomist are not built. They need sip and PyQt4 with dev packages to be installed, otherwise the build system will not build them (they are optional modules for anatomist).
1. Can you run anatomist alone (outside of Brainvisa) ?
2. If yes, do you see the "python" menu in anatomist ? If not, the python bindings are probably missing.
3. You can also print the modules list in Anatomist so we can check what is missing.

Denis
atsui
Posts: 13
Joined: Fri Jan 13, 2012 9:23 pm
Location: Davis, CA USA

Re: missing anatomist module after source build

Post by atsui »

Hi Denis,

It looks like your hypothesis is right. I am able to run anatomist, but there is no python menu. I've attached a screenshot of the modules list from my copy of anatomist. I've compared it to the anatomist from a binary distribution I've downloaded it looks like there are many modules missing.

I have confirmed that I had these packages installed at the time I built BrainVISA: pyqt4-dev-tools python-sip-dev python-qt4-dev

What should I check now?

--Alex
Attachments
anatomistModules.png
anatomistModules.png (43.84 KiB) Viewed 3043 times
Post Reply