Morphologist and Qt driver

[Emppa]

Dear Forum!

I am student starting up a research project about post processing images and 3D reconstruction of the brain in epileptic patients.
I am trying to get morphologist to work on a macOS yosemite. And I have run into a problem when I try to process MRI-pictures, getting the following error, pasted below.
It seems as it does not recognise the Qt driver?

Can anyone help me?

Kind regards Emppa!

Morphologist 2013
Process identifier
morphologist
Execution platform
BrainVISA
Parameters
t1mri = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/Subject1.nii.gz
perform_normalization = False
anterior_commissure = [87.5, 129.29718017600001, 111.71873474100001]
posterior_commissure = [85.704338073700001, 155.034988403, 119.3359375]
interhemispheric_point = [86.278709411600005, 139.05844116200001, 69.570320129400002]
left_hemisphere_point = [107.956626892, 140.27972412099999, 69.570320129400002]
t1mri_nobias = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/nobias_Subject1.nii.gz
histo_analysis = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/nobias_Subject1.han
split_brain = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/segmentation/voronoi_Subject1.nii.gz
left_graph = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/folds/3.1/LSubject1.arg
right_graph = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/folds/3.1/RSubject1.arg
perform_sulci_recognition = False
left_labelled_graph = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/folds/3.1/default_session_auto/LSubject1_default_session_auto.arg
right_labelled_graph = /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/default_analysis/folds/3.1/default_session_auto/RSubject1_default_session_auto.arg
Output
Process Morphologist 2013 started on 2014/12/12 12:49
Skip unselected node: Talairach Transformation


in Morphologist 2013 7 the parameter talairach_transform is not readable or does not exist : /Users/Emppa/Desktop/brainvisa-MacOS-10.5-i386-4.4.0-2013_11_18/Database/subjects/Subject1/t1mri/default_acquisition/registration/RawT1-Subject1_default_acquisition_TO_Talairach-ACPC.trm


RuntimeError
processes.py (2554) in _processExecution:
result = process.execution( self )
processes.py (1204) in execution:
return self._executionNode.run( context )
processes.py (1721) in run:
return self._run( context )
processes.py (2034) in _run:
result.append( node.run( context ) )
processes.py (1721) in run:
return self._run( context )
processes.py (2098) in _run:
return super( ParallelExecutionNode, self )._run( context )
processes.py (2034) in _run:
result.append( node.run( context ) )
processes.py (1721) in run:
return self._run( context )
processes.py (2034) in _run:
result.append( node.run( context ) )
processes.py (1721) in run:
return self._run( context )
processes.py (1921) in _run:
return context.runProcess( self._process )
processes.py (2313) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
processes.py (2285) in _setArguments:
_process.checkArguments()
processes.py (725) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (174) in checkValue:
raise RuntimeError( HTMLMessage(_t_( 'the parameter <em>%s</em> is not readable or does not exist : %s' ) % (unicode(name), unicode(value))) )

Process Morphologist 2013 finished on 2014/12/12 14:36 (1 hours 47 minutes 27 seconds)

[riviere]

Hi,

As I understand from the messages, it has nothing to do with Qt: one processing step is unchecked: the Talairach transformation, so its output is not processed and is missing for the followinf steps.

Apparently you have selected AC/PC manually, and thus do not have used a normalization for image orientation. In this case the Talairach transform step should be ON. I don't know exactly why it is not: normally when you uncheck "perform normalization" in the general pipeline, the Talairach step gets checked. Something went wrong here, but you can certainly re-check it by hand in this case.
(you can skip the steps already done if you re-run the same subject)

Denis

[Emppa]

You are right, somehow Talairach was unchecked.
But I ran it again, and it still cannot locate the QSQLITE driver..

[riviere]

I did not notice a sqlite driver message in your previous log. Sqlite through Qt should not be used in brainvisa (it could only be used through an experimental plugin that is not useful in normal operations), sqlite is used "directly" in python.
So dit the processing run after all, or did it fail ?

[Emppa]

This is the message I am getting from Morphologist:

Process Morphologist 2013 started on 2014/12/14 21:54
OK, the image seems to be in the correct orientation.
QSqlDatabase: QSQLITE driver not loaded QSqlDatabase: available drivers:
QSqlDatabase: QSQLITE driver not loaded
QSqlDatabase: available drivers:
QSqlDatabase: QSQLITE driver not loaded QSqlDatabase: available drivers:

It runs through the process and keep repeating that!

[riviere]

So this Qt pugin is either not found, not loaded, or not initialized, which is somewhat strange and the messages are a bit annoying, but it is probably not harmful since the sqlite plugin in Qt is not needed in the Morphologist pipelines. I just hope other, more useful, plugins are not missing...

Denis

[Emppa]

So how do I bypass this issue. Because I don't get a processed picture when I run morphologist, I get nothing.

[riviere]

Oh, I didn't understand it did not run because you did not say it, and from your first message it seemed that processing was actually running until the Talairach step which was not enabled for you. You know I'm totally blind to your problems, I cannot reproduce them, so you have to be precise on the description.
So I don't know what's happening. You are using MacOs yosemite, which seems to be 10.10 (I had to search on internet, I don't speak macos versions fluently), and we still have only 10.5 as building system, so there may be some incompatibilities

Have you not encountered the problem reported here ? If not I also don't understand why it happens on 10.9 and not on 10.10. MacOS is definitely a strange system full of black magic and non-reproducible behaviours...

However now the strangest thing for me is that on your first message it seemed to run, and stop only after the Taiairach step, and now you say it does not.

Did the first step produce any result the first time ? (bias coorection, histo analysis, brain mask...)