BrainVISA

Hello, I'm trying to understand differences of behavior of the anatomist API between BrainVISA 4.5 and 4.6. With 4.6, linkCursorLastClickedPosition() seems the return positions in the referential currently selected in the view. I have two views of the same volume, one with the referential "t1mr...

And after loading all the objects we need: https://www.dropbox.com/s/un6qpq8atkt4kf5/qpixmap_after.gif?dl=0 Corresponding output in the console: pydev debugger: starting (pid: 215) Headless Anatomist running in normal (non-headless) mode LAUNCHING ELECTRODE LOCATE MAIN NO APP Loading toolbox cortica...

In the attached screen capture, you can see the line responsible of 3 of these errors, the content of the variable diskitem, the IntrAnat interface and the resulting anatomist window (one volume added). (I cannot add images to this post, error message "Could not upload attachment to ./../forum_...

We get 2 or 3 messages of this kind every time we call loadObject(), both for .nii volumes and .gii meshes.

I'm running this from my PyDev debugger.
In the configuration of my interpreter I added brainvisa folders to my python path, $PATH and $LD_LIBRARY_PATH until it works.
Would you suggest a nicer way of proceeding?

Hello

I get hundreds of messages like this when loading objects in anatomist.
Any suggestion?

Thanks
Francois

I added brainvisa/bin to the PATH variable and the errors are gone. It's surprising it didn't cause any problem before... I think I started getting this issue after installing ffmpeg. We do not start the BrainVISA interface from a terminal. Various BrainVISA modules are imported in our Python code, ...

Maybe related also with the way I start BrainVISA... After installing/updating some Ubuntu packages, I get lost of errors when BrainVISA starts. Example: OSError processes.py (5989) in addDir: toolbox=toolbox) # two arguments : process fullpath and category (directories separated by /) processes.py ...

Thanks for the fix and for the info. If it's OK, I'll stick to posting public messages on this forum for now then. I got to this point by starting IntrAnat (this SEEG toolbox developed in Grenoble) from the Eclipse/PyDev debugger. So I guess this is why it doesn't initialize everything as expected. ...

Btw, is this forum the appropriate channel to report this kind of issues?
Or do you have a github on which I could submit issues, or some other bug tracking system?

Hello We have code calling FreeSurfer functions with launchFreesurferCommand > context.system > _system. None of the functions called return properly, because line 3454 returns an error. On my configuration, neuroConfig.brainvisaSysEnv.getVariables() returns None, and own_env.update() is not equippe...

Hello, Any error report triggers the error below on my WSL/Ubuntu 16.04. Missing library libapt-pkg.so.4.12: current version in Ubuntu is 5.0, but it is not part of the BrainVISA distribution. The error can be fixed by installing manually libapt-pkg4.12_1.0.9.8.4_amd64.deb, but there is maybe a bett...

Additional steps: 6) In bash terminal: type "sudo apt-get update && sudo apt-get dist-upgrade" to upgrade all the packages in Ubuntu 7) In bash terminal: type "export DISPLAY=:0" to send the X11 windows to the local MobaXterm X server (add this line to your .bashrc to sav...

Ok thanks.
And it works with the WSL version too

Oh... indeed... I tested so many software configurations that I got mixed up at some point. So the good news is that there is one configuration that actually works! Using WSL+Ubuntu+MobaXterm it is possible to run the linux version of BrainVISA on Windows 10. Here is a summary you could add to your ...