BrainVISA

Thank you so much, Denis!

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

thanks again!

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, exce...

Thank you, Jeff.

The default was set to 'auto'; I changed it to '8' and it worked just fine.

thanks a million!

Dear brainvisers, I am using version 3.1.0 of the segmentation pipeline on a coronal T1 volume. I am getting warning and error messages of the following kind: ----------------------------- ! VIP Warning: Strange: gap of more than 5 points along this trajectory (use smaller scale step) --------------...

Hi Denis el al.,

Any clue regarding what's happening there? thank you!

and the contents of the brainvisa/anatomist log section when using the command line with debugLevel 2 Starting Anatomist..... libaimsvida.so.3.2.1: libaimsvida.so.3.2.1: cannot open shared object file: No such file or directory libaimsdicom.so.3.2.1: libaimsdicom.so.3.2.1: cannot open shared object ...

Here is the contents of the anatomist info window: Data type: object/object - formats : PYTHON XML - Graph sub-formats readers: Generic CorticalFoldArg model_graph roi - AIMS settings: { '__syntax__' : 'aims_settings', 'spm_input_radio_convention' : 1, 'spm_input_spm2_normalization' : 1, 'spm_output...

Alright! Here is the contents of the brainvisa log : starting brainvisa. Note I cannot run BV locally on the linux server:: it's literally a black box that I can access to only remotely. I can also send you the log from one session that works just fine, from another client machine, if you think that...

Thanks Denis, the PyAnatomist modules don't launch when anatomist is called form brainvisa. They are launched properly when anatomist is called from the command line. Here is what I get from launching anatomist with the debugLevel 2. It seems some libraries are not found. But again, it doesn't go th...

Thanks again Denis, when starting anatomist from the command line on this workstation, I see that the config/settings.cfg is loaded and then I see a line specifying that PyAnatomist is present and then a list of modules are loaded. The last message is: all python modules are loaded. It does go that ...

Thank you Denis, I have looked at the brainvisa log and it says that - Anatomist has started (indeed, I see Anatomist's main window pop up) - configuration file is identified: /anatomist/config/settings.cfg but then, that's it, even waiting several minutes does not help. The PyAnatomist module does ...

Hello, I have a somewhat related problem on some of the workstations we are using here. We are running brainvisa 3.2 on a linux server to which we access usinf XP or Unix workstations. On *some* of these latter, we cannot select the AC, PC, IH points because, because anatomist does not load the imag...

Hi Denis;

I had sent the images to Jeff a while ago. Things were working fine under Linux on his side but I am using WinXP. Let me know if you need the images from me again.

thanks

Folks, I think the problem has been identified (and solved), It seems that under my BV incarnation, the voxel size got messed up during the importation from Analyze. As Yann mentioned, the voxel size in the .dim looked fine, not in the .dim.minf, where it had been changed to isotropic values during ...

This weird behavior might be indeed due to bad cache flush between BV sessions. I have launched the pipeline again for bias correction only and now the voxel size has been changed to voxel size: [1.0156000000000001, 1.0156000000000001, 1.3, 1] as BV's message window is now showing. Note that origina...