I'm beginning with BrainVisa and I'm trying to measure the volume of the entire brain, based on T1-weighted images.
However, I'm facing several issues :
- I cannot view the result of the histogram analysis at all... Whenever I try to visualize it, I have an error :
Pb Brainvisa.png (16.6 KiB) Viewed 8656 times
- Besides, since I'm interested in the volume of the entire brain and not only the two hemispheres, I managed to use the comand line "VIPGreyWhiteClassif" to keep the cerebellum. But is there a way to calculate the volume that I get (thanks to a command like Morphometry -> volume, for instance) ?
Could you be more specific ? Which process did you use ?
Is there more information in the log (Brainvisa menu -> show log) ?
You can attach this log file to a post, so we could have a look. See Brainvisa manual to know how to save this log file : http://brainvisa.info/doc/brainvisa-4.0 ... tml#N1093A
I used "Pipeline T1 2007".
The weird thing is, I can go on with the pipeline without any other error (the brain mask for instance seems to be not too bad, but I'd like to be sure). It's just the visualization of the histogram analysis that fails. I don't know if it can have anything to do with the fact that I'm on Windows 7 ?
Here's the log (I hope I saved it well).
This viewer should work also on windows. But we didn't try on Windows 7 because we haven't any computer with this system.
The log file is not readable. Maybe you save it before quitting Brainvisa ? You have to run Brainvisa, run the process that makes an error, then quit Brainvisa and after that, you can send the log file.
Actually, I have a brainvisa4.log (which is the text file that I'm sending to you) and a brainvisa4.log~ (which is a log~). When I try to attach the .log~, there's a message "the extension log~ is not allowed.
I checked the log directly though, and the message is the same than in the image I posted earlier.
PS : apart from this functionality, BrainVisa seems to be working well enough on Windows 7
Ok, the log file was correct this time. But indeed, it doesn't give much more information...
I don't understand why it doesn't work, especially when all the pipeline runs without errors.
I tried the process on a windows computer, there wasn't any error.
Maybe you can send me by private message the t1 mri that you processed and I'll try on my computer to see if it is related to the file ?
Meanwhile, if you need information from the histogram analysis, you can open the histogram file with a text editor to see its content...
I tried to process the image you send me and didn't have any problem to see the histogram with Linux and Windows version. So the error doesn't seem to be linked to the image. Maybe it is an incompatibility of the windows package with Windows 7 ? I haven't any machine with this system so I cannot test...
Do you have another computer with another system ?
Well, I guess it is an incompatibility with my Windows version then.
I have other computers with Windows XP or Linux, I will try the image when I get the chance to install BrainVisa on them. It isn't that urgent since the rest of the process is working well.
Just so you know, BrainVisa keeps on "crashing" and I have to reload it several times during the day, maybe it has stability problems with Windows 7 too.
Basically,
if the brain mask looks OK, I do not think you will get additional information
visualizing the histogram analysis. To be honest this is mainly
dedicated to wizards... The good news is that the next release will
include a more robust version of this analysis that shall overcome
most of the difficulties of the past.
We are working now on the brain segmentation...
I am trying to use T1 segmentation pipeline (brainVISA 4 for windows (16/6/2010). Data analysis is stopped at histogram analysis with the following error log:
Also using BrainVISA 3 up to now I segemented about 15 subjects and I had problems with histo analysis in about 1/3 of them. Does anyone has any advice how to eliminate this error during analysis systematically?
Thanks for any help!
Marcel
ERROR LOG:
Process T1 Pipeline 2007 1 started on 2010/07/15 11:28
 Left hemisphere point not specified - X axis flip will not be checked
OK, the image seems to be in the correct orientation.

in Vip Histogram analysis 1 System command exited with non null value : 111
RuntimeError
neuroProcesses.py (1950) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (65) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'n', '-m', 'a', '-u', self.undersampling, '-g', 's' )
neuroProcessesGUI.py (1457) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2055) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in Histogram analysis 1 System command exited with non null value : 111
RuntimeError
neuroProcesses.py (1950) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1322) in run:
return self._run( context )
neuroProcesses.py (1635) in _run:
return node.run( context )
neuroProcesses.py (1322) in run:
return self._run( context )
neuroProcesses.py (1435) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1766) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1950) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (65) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'n', '-m', 'a', '-u', self.undersampling, '-g', 's' )
neuroProcessesGUI.py (1457) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2055) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

in T1 Pipeline 2007 1 System command exited with non null value : 111
RuntimeError
neuroProcesses.py (1950) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1322) in run:
return self._run( context )
neuroProcesses.py (1508) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1322) in run:
return self._run( context )
neuroProcesses.py (1435) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1766) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1950) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1322) in run:
return self._run( context )
neuroProcesses.py (1635) in _run:
return node.run( context )
neuroProcesses.py (1322) in run:
return self._run( context )
neuroProcesses.py (1435) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1766) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (1950) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (65) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullPath(), '-o',self.histo_analysis.fullPath(), '-S', 'n', '-m', 'a', '-u', self.undersampling, '-g', 's' )
neuroProcessesGUI.py (1457) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2055) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )
