EMSegmenter problem

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

EMSegmenter problem

Tae-young
Hi

I want to use EMSegmenter for segment full part of the head like eyes, bone
of neck & head, and brain

But during the used EMSegmenter with atlas modules I got some same error
message continuously ,,
"Pre-processing did not execute correctly!"
Like this



<http://slicer-users.65878.n3.nabble.com/file/n4031439/%E1%84%89%E1%85%B3%E1%84%8F%E1%85%B3%E1%84%85%E1%85%B5%E1%86%AB%E1%84%89%E1%85%A3%E1%86%BA_2016-12-15_%E1%84%8B%E1%85%A9%E1%84%8C%E1%85%A5%E1%86%AB_4.png>



Thus,what is the problem? and how can I prevent to this problem??

Best regards.

P.S I used 3D Slicer 4.3.1 - 1 MACOSX ver.

 



--
View this message in context: http://slicer-users.65878.n3.nabble.com/EMSegmenter-problem-tp4031439.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: EMSegmenter problem

Kilian Pohl
please start slicer from a command line similar to

./Slicer &> blub.log

Go through all the steps and then send the log file

Kilian



On 12/14/2016 11:36 AM, Tae-young wrote:

> Hi
>
> I want to use EMSegmenter for segment full part of the head like eyes, bone
> of neck & head, and brain
>
> But during the used EMSegmenter with atlas modules I got some same error
> message continuously ,,
> "Pre-processing did not execute correctly!"
> Like this
>
>
>
> <http://slicer-users.65878.n3.nabble.com/file/n4031439/%E1%84%89%E1%85%B3%E1%84%8F%E1%85%B3%E1%84%85%E1%85%B5%E1%86%AB%E1%84%89%E1%85%A3%E1%86%BA_2016-12-15_%E1%84%8B%E1%85%A9%E1%84%8C%E1%85%A5%E1%86%AB_4.png>
>
>
>
> Thus,what is the problem? and how can I prevent to this problem??
>
> Best regards.
>
> P.S I used 3D Slicer 4.3.1 - 1 MACOSX ver.
>
>    
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/EMSegmenter-problem-tp4031439.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: EMSegmenter problem

Tae-young
*This is the Log from EMsegmenter.
The red sign end of the script is error.

Thank you for your help

Best regards
Tae-Young*



Python 2.7.10 (default, Nov 12 2015, 13:06:14)
[GCC 4.2.1 Compatible Clang 3.1 ((tags/RELEASE_31/final))] on darwin


>>> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'CT Hand Bone'
>>> File :
>>> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/CT-Hand-Bone.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain Full
Parcellation' File :
'/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain
Hemisphere' File :
'/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Hemisphere.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain
Parcellation' File :
'/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Parcellation.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain'
File :
'/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'Non Human Primate'
File :
'/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/Non-Human-Primate.mrml'
[EMSegmentPy 12/15/2016 15:46:58]: Attempting to load task 'MRI Human Brain
Full Parcellation' from file
'/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 12/15/2016 15:47:01]: Loading completed.
Error executing __tpycl_result = __tmpdoc =
vtkImageThreshold0x145fc39b0.SetInput.__doc__
(<type 'exceptions.AttributeError'>, AttributeError('SetInput',), <traceback
object at 0x145ff1638>)


while executing
"py_eval "__tmpdoc = $pyInstanceName.$method.__doc__""
(procedure "tpycl::methodCaller" line 35)
invoked from within
"tpycl::methodCaller vtkImageThreshold0x145fc39b0
vtkImageThreshold0x145fc39b0 $args"
(procedure "vtkImageThreshold0x145fc39b0" line 1)
invoked from within
"$thresh SetInput $inputVolume"
(procedure "RemoveNegativeValues" line 37)
invoked from within
"RemoveNegativeValues $inputTargetNode"
(procedure "InitPreProcessing" line 44)
invoked from within
"InitPreProcessing"
(procedure "::EMSegmenterPreProcessingTcl::Run" line 20)
invoked from within
"::EMSegmenterPreProcessingTcl::Run”


Traceback (most recent call last):
File
"/Applications/Slicer.app/Contents/lib/Slicer-4.5/qt-loadable-modules/Python/EMSegmentWizard/EMSegmentDefineMiscParametersStep.py",
line 155, in onEntry
self.loadFromMRML()
File
"/Applications/Slicer.app/Contents/lib/Slicer-4.5/qt-loadable-modules/Python/EMSegmentWizard/EMSegmentDefineMiscParametersStep.py",
line 223, in loadFromMRML
if self.__roiWidget:
AttributeError: ctkWorkflowWidgetStep has no attribute named
'_EMSegmentDefineMiscParametersStep__roiWidget'



--
View this message in context: http://slicer-users.65878.n3.nabble.com/EMSegmenter-problem-tp4031440p4031443.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
Reply | Threaded
Open this post in threaded view
|

Re: EMSegmenter problem

Tae-young
This post has NOT been accepted by the mailing list yet.
In reply to this post by Kilian Pohl
This is the Log from EMsegmenter.
The red sign end of the script is error.

Thank you for your help

Best regards
Tae-Young




Python 2.7.10 (default, Nov 12 2015, 13:06:14)
[GCC 4.2.1 Compatible Clang 3.1 ((tags/RELEASE_31/final))] on darwin


>>> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'CT Hand Bone' File : '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/CT-Hand-Bone.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain Full Parcellation' File : '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain Hemisphere' File : '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Hemisphere.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain Parcellation' File : '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Parcellation.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain' File : '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.mrml'
[EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'Non Human Primate' File : '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/Non-Human-Primate.mrml'
[EMSegmentPy 12/15/2016 15:46:58]: Attempting to load task 'MRI Human Brain Full Parcellation' from file '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 12/15/2016 15:47:01]: Loading completed.
Error executing __tpycl_result = __tmpdoc = vtkImageThreshold0x145fc39b0.SetInput.__doc__
(<type 'exceptions.AttributeError'>, AttributeError('SetInput',), <traceback object at 0x145ff1638>)


while executing
"py_eval "__tmpdoc = $pyInstanceName.$method.__doc__""
(procedure "tpycl::methodCaller" line 35)
invoked from within
"tpycl::methodCaller vtkImageThreshold0x145fc39b0 vtkImageThreshold0x145fc39b0 $args"
(procedure "vtkImageThreshold0x145fc39b0" line 1)
invoked from within
"$thresh SetInput $inputVolume"
(procedure "RemoveNegativeValues" line 37)
invoked from within
"RemoveNegativeValues $inputTargetNode"
(procedure "InitPreProcessing" line 44)
invoked from within
"InitPreProcessing"
(procedure "::EMSegmenterPreProcessingTcl::Run" line 20)
invoked from within
"::EMSegmenterPreProcessingTcl::Run”


Traceback (most recent call last):
File "/Applications/Slicer.app/Contents/lib/Slicer-4.5/qt-loadable-modules/Python/EMSegmentWizard/EMSegmentDefineMiscParametersStep.py", line 155, in onEntry
self.loadFromMRML()
File "/Applications/Slicer.app/Contents/lib/Slicer-4.5/qt-loadable-modules/Python/EMSegmentWizard/EMSegmentDefineMiscParametersStep.py", line 223, in loadFromMRML
if self.__roiWidget:
AttributeError: ctkWorkflowWidgetStep has no attribute named '_EMSegmentDefineMiscParametersStep__roiWidget'
Reply | Threaded
Open this post in threaded view
|

Re: EMSegmenter problem

Kilian Pohl
In reply to this post by Tae-young
Is this the entire log file from when Slicer started ? If not could you
send this please
Have you defined an input volume ?
What are the exact steps you did to get to this log ?



On 12/14/2016 10:59 PM, Tae-young wrote:

> *This is the Log from EMsegmenter.
> The red sign end of the script is error.
>
> Thank you for your help
>
> Best regards
> Tae-Young*
>
>
>
> Python 2.7.10 (default, Nov 12 2015, 13:06:14)
> [GCC 4.2.1 Compatible Clang 3.1 ((tags/RELEASE_31/final))] on darwin
>
>
>>>> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'CT Hand Bone'
>>>> File :
>>>> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/CT-Hand-Bone.mrml'
> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain Full
> Parcellation' File :
> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain
> Hemisphere' File :
> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Hemisphere.mrml'
> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain
> Parcellation' File :
> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Parcellation.mrml'
> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'MRI Human Brain'
> File :
> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.mrml'
> [EMSegmentPy 12/15/2016 15:46:53]: Added to List Task: 'Non Human Primate'
> File :
> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/Non-Human-Primate.mrml'
> [EMSegmentPy 12/15/2016 15:46:58]: Attempting to load task 'MRI Human Brain
> Full Parcellation' from file
> '/var/folders/9t/qp640qrn3j13ssvdxvk7db_80000gn/T/Slicer/EMSegmentTaskCopy/MRI-Human-Brain-Full-Parcellation.mrml'
> [EMSegmentPy 12/15/2016 15:47:01]: Loading completed.
> Error executing __tpycl_result = __tmpdoc =
> vtkImageThreshold0x145fc39b0.SetInput.__doc__
> (<type 'exceptions.AttributeError'>, AttributeError('SetInput',), <traceback
> object at 0x145ff1638>)
>
>
> while executing
> "py_eval "__tmpdoc = $pyInstanceName.$method.__doc__""
> (procedure "tpycl::methodCaller" line 35)
> invoked from within
> "tpycl::methodCaller vtkImageThreshold0x145fc39b0
> vtkImageThreshold0x145fc39b0 $args"
> (procedure "vtkImageThreshold0x145fc39b0" line 1)
> invoked from within
> "$thresh SetInput $inputVolume"
> (procedure "RemoveNegativeValues" line 37)
> invoked from within
> "RemoveNegativeValues $inputTargetNode"
> (procedure "InitPreProcessing" line 44)
> invoked from within
> "InitPreProcessing"
> (procedure "::EMSegmenterPreProcessingTcl::Run" line 20)
> invoked from within
> "::EMSegmenterPreProcessingTcl::Run”
>
>
> Traceback (most recent call last):
> File
> "/Applications/Slicer.app/Contents/lib/Slicer-4.5/qt-loadable-modules/Python/EMSegmentWizard/EMSegmentDefineMiscParametersStep.py",
> line 155, in onEntry
> self.loadFromMRML()
> File
> "/Applications/Slicer.app/Contents/lib/Slicer-4.5/qt-loadable-modules/Python/EMSegmentWizard/EMSegmentDefineMiscParametersStep.py",
> line 223, in loadFromMRML
> if self.__roiWidget:
> AttributeError: ctkWorkflowWidgetStep has no attribute named
> '_EMSegmentDefineMiscParametersStep__roiWidget'
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/EMSegmenter-problem-tp4031440p4031443.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

_______________________________________________
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
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ