Sulci recognition with SPAM

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joycechen
Posts: 2
Joined: Mon Jan 24, 2011 3:52 pm

Sulci recognition with SPAM

Post by joycechen »

Hello,

I'm a new user and am not sure if I have set up things properly in order to run Sulci recognition with SPAM (global + local). I have run the T1 Pipeline 2007, but when the analysis gets to the Sulci recognition section, I get the error message below. I am wondering if perhaps the global and local packages that I downloaded were not placed in the correct directories?

brainvisa/share/shfj-4.0/models/descriptive_models/
there are:
labels_priors/
segments_relations/

I've added the directory segments/ and put in here, the downloaded materials:
global_registered_spam_left/
global_registered_spam_right/
locally_from_global_registred_spam_left/
locally_from_global_registred_spam_right/

Perhaps this is not the right place and therefore I get the following error below:

in SPAM-based 1 argument model is mandatory

Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )




in Sulci Recognition (left side) 1 argument model is mandatory


Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )




in Sulci Recognition (both hemispheres) 1 argument model is mandatory


Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1575) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )




in T1 Pipeline 2007 1 argument model is mandatory


Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1575) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )



*****
Thank you for your time and any advice you can provide!

Best,
Joyce
Dominique Geffroy
Site Admin
Posts: 161
Joined: Thu Mar 01, 2007 4:22 pm
Location: IFR 49 - Neurospin, Gif-sur-Yvette, France
Contact:

Re: Sulci recognition with SPAM

Post by Dominique Geffroy »

Hello,

It seems that you copied the models at the right place. Maybe you forgot to update brainvisa shared database after that ? To do so, you can run the brainvisa process data management -> update databases. Check the shared database : brainvisa/share/shfj-4.0 and click on update. Or instead, you can run again the setup program.

Dominique
joycechen
Posts: 2
Joined: Mon Jan 24, 2011 3:52 pm

Re: Sulci recognition with SPAM

Post by joycechen »

Hi Dominique,

Thanks for your quick reply. I updated the database, and also ran the setup program again, but it didn't seem to do the trick. Do the files in the global and local models have to be unzipped? I can't think of anything else to check. Thanks for your advice.

Joyce

The error message is:

in SPAM-based 1 argument model is mandatory

Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )




in Sulci Recognition (left side) 1 argument model is mandatory


Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )




in Sulci Recognition (both hemispheres) 1 argument model is mandatory


Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1575) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )




in T1 Pipeline 2007 1 argument model is mandatory


Exception
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1575) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1828) in runProcess:
apply( self._setArguments, (_process,)+args, kwargs )
neuroProcesses.py (1813) in _setArguments:
_process.checkArguments()
neuroProcesses.py (418) in checkArguments:
o.checkValue( p, getattr( self, p, None ) )
readdiskitem.py (139) in checkValue:
Parameter.checkValue( self, name, value )
neuroData.py (93) in checkValue:
raise Exception( HTMLMessage(_t_('argument <em>%s</em> is mandatory') % name) )
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Re: Sulci recognition with SPAM

Post by riviere »

Hi,
In the SPAM recognition processes (either from the T1 pipeline, or using them individually from sulci/morphometry/SPAM/SPAM recognition*, do you have something as the "model" parameter ? If not, do you see available models for that parameter when clicking on the greed database button ?

(in the next version, downloading and installing the SPAM models will be done via a dedicated process, so it will be easier)

Denis
Dominique Geffroy
Site Admin
Posts: 161
Joined: Thu Mar 01, 2007 4:22 pm
Location: IFR 49 - Neurospin, Gif-sur-Yvette, France
Contact:

Re: Sulci recognition with SPAM

Post by Dominique Geffroy »

Hi,

To sum up, after installing the models you should have in you brainvisa package in share/shfj-4.0/models/descriptive_models/segments :

descriptive_models/segments/global_registered_spam_left:
meshes/ spam_distribs/ spam_distribs.dat spam_distribs.dat.minf subjects_transformations/

descriptive_models/segments/global_registered_spam_right:
meshes/ spam_distribs/ spam_distribs.dat spam_distribs.dat.minf subjects_transformations/

descriptive_models/segments/locally_from_global_registred_spam_left:
bingham_direction_trm_priors/ gaussian_translation_trm_priors.dat local_referentials.dat~ spam_distribs.dat vonmises_angle_trm_priors.dat
bingham_direction_trm_priors.dat gaussian_translation_trm_priors.dat.minf local_referentials.dat.minf spam_distribs.dat.minf vonmises_angle_trm_priors.dat.minf
bingham_direction_trm_priors.dat.minf local_referentials/ meshes/ subjects_transformations/
gaussian_translation_trm_priors/ local_referentials.dat spam_distribs/ vonmises_angle_trm_priors/

descriptive_models/segments/locally_from_global_registred_spam_right:
bingham_direction_trm_priors/ gaussian_translation_trm_priors.dat local_referentials.dat~ spam_distribs.dat vonmises_angle_trm_priors.dat
bingham_direction_trm_priors.dat gaussian_translation_trm_priors.dat.minf local_referentials.dat.minf spam_distribs.dat.minf vonmises_angle_trm_priors.dat.minf
bingham_direction_trm_priors.dat.minf local_referentials/ meshes/ subjects_transformations/
gaussian_translation_trm_priors/ local_referentials.dat spam_distribs/ vonmises_angle_trm_priors/

descriptive_models/segments/talairach_spam_left:
meshes/ spam_distribs/ spam_distribs.dat spam_distribs.dat.minf

descriptive_models/segments/talairach_spam_right:
meshes/ spam_distribs/ spam_distribs.dat spam_distribs.dat.minf

If it is not the case, maybe you forgot to install one of the required models. Check the documentation of the spam recognition process : http://brainvisa.info/doc/brainvisa-4.0 ... ition.html to see if you have downloaded and installed all the files indicated.

Dominique
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