EM Segmenter-MRI Full Parcellation

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EM Segmenter-MRI Full Parcellation

vidhya kamakshi
Hi,

I am using slicer 4.0.1 (10.1.2012) 64bit windows 7 system. 
EM segmentation with atlas (MRI Full Parcellation task) is not working.  
It gives some messages in the error log like-

Traceback (most recent call last):

File "C:/Program Files (x86)/Slicer 4.0.1.2012-01-10/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentStartSegmentationStep.py", line 54, in onEntry

message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while the segmentation runs..", qt.QMessageBox.Ignore )

ValueError: Could not find matching overload for given arguments:

(0, 'Please wait', 'Please wait while the segmentation runs..', 1048576)

The following slots are available:

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons, QWidget* parent, Qt::WindowFlags flags)

QMessageBox* QMessageBox()

QMessageBox* QMessageBox(QWidget* parent)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons, QWidget* parent)


Kindly help.


Thanking You


Regards

Vidhya


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Re: EM Segmenter-MRI Full Parcellation

madanrao
Hello Vidhya,

There might be some memory related problems with QT (1048576)

Generally, using slicer module EM Segmenter for brain parcellation is complex and difficult to
understand.

I advise try an earlier stable version (online tutorials and earlier posts on this forum help you).

After a while I worked with some success on its command line version.

I am giving you the code here:

"C:/Program Files/Slicer3 3.2.2008-08-08/Slicer3.exe" --launch EMSegmentCommandLine.exe --mrmlSceneFileName C:/Segmentation/brain/42210/42210/SPL_PNL_2009/trial3/EMSegmenterScene.mrml --targetVolumeFileNames C:/Segmentation/brain/case3/case3_mribfc_cast.nrrd --atlasVolumeFileNames C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Atlas_subcortical_nuclei_cast.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Atlas_whitematter_BS_CBM_cast.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/MPRAGE_CORRECTED_CAST.nrrd --intermediateResultsDirectory C:/Library/Brain/trials/case3/output

I hope this helps.

AM Mohan Rao

On Mon, Jan 23, 2012 at 11:47 AM, vidhya kamakshi <[hidden email]> wrote:
Hi,

I am using slicer 4.0.1 (10.1.2012) 64bit windows 7 system. 
EM segmentation with atlas (MRI Full Parcellation task) is not working.  
It gives some messages in the error log like-

Traceback (most recent call last):

File "C:/Program Files (x86)/Slicer 4.0.1.2012-01-10/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentStartSegmentationStep.py", line 54, in onEntry

message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while the segmentation runs..", qt.QMessageBox.Ignore )

ValueError: Could not find matching overload for given arguments:

(0, 'Please wait', 'Please wait while the segmentation runs..', 1048576)

The following slots are available:

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons, QWidget* parent, Qt::WindowFlags flags)

QMessageBox* QMessageBox()

QMessageBox* QMessageBox(QWidget* parent)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons, QWidget* parent)


Kindly help.


Thanking You


Regards

Vidhya


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Re: EM Segmenter-MRI Full Parcellation

Kilian Pohl
Hi Vidhya,

I agree with Madan. The error seems to be cause by QT and could be linked to low memory. Just so you know the algorithm of the EMSegmenter has not changed in a longer time only the user interface . So you probably have more luck with earlier stable version of Slicer .


Kilian




On 1/23/2012 2:26 AM, Madan Rao wrote:
Hello Vidhya,

There might be some memory related problems with QT (1048576)

Generally, using slicer module EM Segmenter for brain parcellation is complex and difficult to
understand.

I advise try an earlier stable version (online tutorials and earlier posts on this forum help you).

After a while I worked with some success on its command line version.

I am giving you the code here:

"C:/Program Files/Slicer3 3.2.2008-08-08/Slicer3.exe" --launch EMSegmentCommandLine.exe --mrmlSceneFileName C:/Segmentation/brain/42210/42210/SPL_PNL_2009/trial3/EMSegmenterScene.mrml --targetVolumeFileNames C:/Segmentation/brain/case3/case3_mribfc_cast.nrrd --atlasVolumeFileNames C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Background.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Atlas_subcortical_nuclei_cast.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/Atlas_whitematter_BS_CBM_cast.nrrd,C:/Segmentation/brain/42210/42210/SPL_PNL_2009/input_files/CL/MPRAGE_CORRECTED_CAST.nrrd --intermediateResultsDirectory C:/Library/Brain/trials/case3/output

I hope this helps.

AM Mohan Rao

On Mon, Jan 23, 2012 at 11:47 AM, vidhya kamakshi <[hidden email]> wrote:
Hi,

I am using slicer 4.0.1 (10.1.2012) 64bit windows 7 system. 
EM segmentation with atlas (MRI Full Parcellation task) is not working.  
It gives some messages in the error log like-

Traceback (most recent call last):

File "C:/Program Files (x86)/Slicer 4.0.1.2012-01-10/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentStartSegmentationStep.py", line 54, in onEntry

message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while the segmentation runs..", qt.QMessageBox.Ignore )

ValueError: Could not find matching overload for given arguments:

(0, 'Please wait', 'Please wait while the segmentation runs..', 1048576)

The following slots are available:

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons, QWidget* parent, Qt::WindowFlags flags)

QMessageBox* QMessageBox()

QMessageBox* QMessageBox(QWidget* parent)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons)

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString text, QMessageBox::StandardButtons buttons, QWidget* parent)


Kindly help.


Thanking You


Regards

Vidhya


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



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Re: EM Segmenter-MRI Full Parcellation

Daniel Haehn
In reply to this post by vidhya kamakshi
Hi Vidhya,

looking at the error message: it should work since this API call should be used:

QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title,
QString text, QMessageBox::StandardButtons buttons)

Which Qt version are you using?

The value 1048576 should be only the constant qt.QMessageBox.Ignore
which means just one 'ignore' button.

Also, it would be safe to comment the line 54 in C:/Program Files
(x86)/Slicer 4.0.1.2012-01-10/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentStartSegmentationStep.py
since this is only a message box.

Cheers,
Daniel

On Mon, Jan 23, 2012 at 1:17 AM, vidhya kamakshi <[hidden email]> wrote:

> Hi,
>
> I am using slicer 4.0.1 (10.1.2012) 64bit windows 7 system.
> EM segmentation with atlas (MRI Full Parcellation task) is not working.
> It gives some messages in the error log like-
>
> Traceback (most recent call last):
>
> File "C:/Program Files (x86)/Slicer
> 4.0.1.2012-01-10/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentStartSegmentationStep.py",
> line 54, in onEntry
>
> message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait
> while the segmentation runs..", qt.QMessageBox.Ignore )
>
> ValueError: Could not find matching overload for given arguments:
>
> (0, 'Please wait', 'Please wait while the segmentation runs..', 1048576)
>
> The following slots are available:
>
> QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString
> text, QMessageBox::StandardButtons buttons, QWidget* parent, Qt::WindowFlags
> flags)
>
> QMessageBox* QMessageBox()
>
> QMessageBox* QMessageBox(QWidget* parent)
>
> QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString
> text)
>
> QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString
> text, QMessageBox::StandardButtons buttons)
>
> QMessageBox* QMessageBox(QMessageBox::Icon icon, QString title, QString
> text, QMessageBox::StandardButtons buttons, QWidget* parent)
>
>
> Kindly help.
>
>
> Thanking You
>
>
> Regards
>
> Vidhya
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
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