Calling "Import FreeSurfer grey/white segmentation to Morphologist" from a script

[francois]

Hello,

I'm trying to call "Import FreeSurfer grey/white segmentation to Morphologist" from a Python script, but I don't know how to get the links propagated.
If I use the BrainVISA interface, I can select T1_orig and T1_output only, and all the other linked parameters are filled automatically.
How do I get the same thing from a script, using runProcess?

Code: Select all

self.brainvisaContext.runInteractiveProcess(None, 'Import FreeSurfer grey/white segmentation to Morphologist', T1_orig=..., T1_output=...)
self.brainvisaContext.runProcess('Import FreeSurfer grey/white segmentation to Morphologist', T1_orig=..., T1_output=...)

Exception: Mandatory argument <em>ribbon_image</em> has no value

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processImport = getProcessInstance('Import FreeSurfer grey/white segmentation to Morphologist')
processImport.setValue('T1_orig', ...)
processImport.setValue('T1_output', ...)
self.brainvisaContext._processExecution(processImport)

This seems to fill all the parameters correctly, but crashes at the first call to launchFreesurferCommand():

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on
2018/05/18 18:52
Convert .mgz to .nii with FreeSurfer
ERROR in Import FreeSurfer grey/white segmentation to Morphologist 1 FreeSurfer
not available or one freesurfer command line has failed. Please see the log file
in the main menu of BrainVISA for more information.

I tried so many different combinations of things, and couldn't get this to work. But if I run it interactively from BrainVISA, it works...

Thanks
François

[riviere]

Hi,
It should normally work as you had expected but it may behave differently if databases have been disabled at startup in your script. As I don't know how it starts, I cannot really tell...
If databases are enabled and setup (you need a Freesurfer database and a Morphologist database for the process you want to use), completion should take place in any of the following uses:

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contex.runProcess('Import_FROM_FreeSurfer_TO_Morpho', T1_orig=..., T1_output=...)

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proc = getProcessInstance('Import_FROM_FreeSurfer_TO_Morpho')
proc.T1_orig = ...
proc.T1_output = ...
# at this point other parameters should be already filled and can be print
context.runProcess(proc)

Code: Select all

proc = getProcessInstance('Import_FROM_FreeSurfer_TO_Morpho')
context.runProcess(proc, , T1_orig=..., T1_output=...)

The paths you are using should be valid within the selected databases (and should not be symlinks with different paths even if they end up to the same files).
Denis

[francois]

I found my error:
I was passing the orig.mgz from a folder that was not in the local freesurfer database. No wonder it was not finding the associated files...

Well, at least now I know in details all the ways to call processes and pass them parameters

Thanks
Francois