BrainVISA

Hi,

I'm wondering whether there's an option to launch a .bvproc from the command line (i.e without having to launch the brainvisa interface)... I've looked at the options (BrainVISA --help) but I didn't see anything to do this...

Thanks,

Sylvain

Hi Sylvain,
Oh, that's right the "-r" option is not documented... Thanks to point it out...
So, there are 3 ways to run a .bvproc in a commandline:
- The "old" way:

If your process.bvproc has all parameters configured and the execution does not rely on databasing, you can add the -f option to start faster.
This method starts the full (or almost full) brainvisa infrastructure before running the process.[/*]
- The "new" way:

This methods tries to be more minimalist and thus faster to start. It disables databasing and other things by default (unless you pass the --enabledb option), and uses a "processes cache" to avoid reading them all.
- the convenience script axon-runprocess does the same as the "new way", through a script, which may (or may not) appear easier to run.

In all cases, a process can be specified either by a .bvproc file, or a process name and series of arguments, for instance:

Denis

thanks, Denis!

Hi Denis,

I tried running this command - as described by you :

.

I get the following error -



Can you let me know what is going on? I think morphologist needs at least 14 arguments.

Thank you,
Durai

Hi,

The completion of output file names has not worked.
I see two possible reasons:
- maybe the relative file name is not supported with databasing (I haven't checked), you can try using an absolute path (since the databasing and completion system needs to identify databases by the beginning of the path.
- or you haven't setup a database and imported the raw MRI into it. From your example with a relative file name, I cannot see if the image is in a brainvisa/morphologist directory tree organization or not, here.

Denis