Re: EMsegmenter would not work

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Re: EMsegmenter would not work

Kilian Pohl
Hi Renjie,

On 4/26/2012 10:24 AM, He,Renjie wrote:
> Dear Kilian,
>
> I did all you mentioned, after run the simple segmentation on version 4.1.0, after a flash of altas on screen, it gives the same message: "segmentation did not execute correctly!".
>
> The files generated during segmentation procedures are: pos files, aligned altas files, aligned t1 file, but deformVolume and EM_map are empty.
Are you running simple or advanced mode ? If you ran it in simple mode
could you switch to advance mode and let me know exactly after which
step you get an error message ?

Did you delete the directory ? Could you just send me the log that lists
all the tasks that are added to the list similar to

[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
File :

...
in my previous email

Thanks

Kilian




>
> Renjie
>
>
> ________________________________________
> From: Kilian Pohl [[hidden email]]
> Sent: Wednesday, April 25, 2012 6:56 PM
> To: He,Renjie
> Subject: Re: EMsegmenter would not work
>
> Hi Renjie,
>
> I assume you run into this problem when you run Slicer 4.1.0 and not
> 4.0.1- correct ? I just installed it on my machine and it runs fine .
> One thing I noticed is that you have in
>
> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\
>
> a couple of tasks that are not valid anymore . Could you do me a favour and remove the file
>
> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy
>
> and restart Slicer as well as run the EMSegmenter ?
>
> The directory should list the following mrml files :
>
> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
> File :
> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
> Full Parcellation'  File :
> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
> Hemisphere'  File :
> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
> Parcellation'  File :
> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
> Brain'  File :
> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
> Primate'  File :
> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
> GetTclTaskDirectory::Copying task files ...
>       from: D:/pieper/Slicer4.1/Slicer
> 4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
>       to: C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy
>
> Also do you mind if I post the next message on the slicer devel list so
> that other can follow the track too ? Ron asked me to do that
>
> Kilian
>
>
> On 04/16/2012 06:06 PM, He,Renjie wrote:
>> Thanks for your attention!
>>
>> ________________________________________
>> From: Kilian Pohl [[hidden email]]
>> Sent: Monday, April 16, 2012 4:57 PM
>> To: He,Renjie
>> Subject: Re: EMsegmenter would not work
>>
>> This helps a lot - I will further investigate next week
>>
>> Kilian
>>
>>
>>
>> On 4/16/2012 10:06 AM, He,Renjie wrote:
>>> Dear Kilian,
>>>
>>> Thank you so much for your time and help!
>>>
>>> Here is the message for version 4.1.0 : "segmentation did not execute correctly!".
>>> and log error:
>>> ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line 2162
>>> vtkEMSegmentLogic (1E2E6F10): Exception thrown during segmentation: bad allocation
>>>
>>>
>>>
>>> Here is the log for version 4.0.1 :
>>>
>>> Show module (name): "EMSegment"
>>> onEntryInternal - entering input from 1. Define Task
>>> processingAfterOnEntry
>>> showUserInterface - showing 1. Define Task
>>>
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand Bone'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human Eye'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion Exp'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Exp'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Full Parcellation'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Hemisphere'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain HIPR'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Parcellation'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human Primate'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas Cluster'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>
>>> goForward - posting ValidationTransition
>>> attemptToGoToNextStep - Attempting to go to the next step
>>> validateInternal - validating input from 1. Define Task
>>>
>>> [EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI Human Brain' from file 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>
>>> ==========================================================================
>>> == Completed importing data C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
>>> ==========================================================================
>>> BiasCorrectionType: 0
>>> UseLLS_Recompute_Means: 0
>>> BiasCorrectionType: 0
>>> UseLLS_Recompute_Means: 0
>>> BiasCorrectionType: 0
>>> UseLLS_Recompute_Means: 0
>>> [EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>
>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>> performTransitionBetweenSteps - Performing transition between steps
>>> onExitInternal - exiting 1. Define Task
>>> onEntryInternal - entering input from 2. Define Input Datasets
>>> processingAfterOnEntry
>>> updateClientArea - hiding 1. Define Task
>>> showUserInterface - showing 2. Define Input Datasets
>>>
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>> Sourcing general Task file : C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>> Sourcing task specific file: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>
>>> goToStep - Attempting to go to finish step Segment
>>> goForward - posting ValidationTransition
>>> attemptToGoToNextStep - Attempting to go to the next step
>>> validateInternal - validating input from 2. Define Input Datasets
>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>> performTransitionBetweenSteps - Performing transition between steps
>>> onExitInternal - exiting 2. Define Input Datasets
>>> onEntryInternal - entering input from 3. Define Anatomical Tree
>>> processingAfterOnEntry
>>> goForward - posting ValidationTransition
>>> attemptToGoToNextStep - Attempting to go to the next step
>>> validateInternal - validating input from 3. Define Anatomical Tree
>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>> performTransitionBetweenSteps - Performing transition between steps
>>> onExitInternal - exiting 3. Define Anatomical Tree
>>> onEntryInternal - entering input from 4. Define Atlas
>>> processingAfterOnEntry
>>> goForward - posting ValidationTransition
>>> attemptToGoToNextStep - Attempting to go to the next step
>>> validateInternal - validating input from 4. Define Atlas
>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>> performTransitionBetweenSteps - Performing transition between steps
>>> onExitInternal - exiting 4. Define Atlas
>>> onEntryInternal - entering input from 5. Edit Registration Parameters
>>> processingAfterOnEntry
>>> goForward - posting ValidationTransition
>>> attemptToGoToNextStep - Attempting to go to the next step
>>> validateInternal - validating input from 5. Edit Registration Parameters
>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>> performTransitionBetweenSteps - Performing transition between steps
>>> onExitInternal - exiting 5. Edit Registration Parameters
>>> onEntryInternal - entering input from 6. Define Preprocessing
>>> processingAfterOnEntry
>>> goForward - posting ValidationTransition
>>>
>>>
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>
>>> Sourcing general Task file : C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>> Sourcing task specific file: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>
>>> GetTclTaskDirectory::Copying task files ...
>>>     from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>> Sourcing general Task file : C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>> Sourcing task specific file: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>> couldn't read file "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl": no such file or directory
>>> couldn't read file "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl": no such file or directory
>>>        while executing
>>> "source C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
>>> TCL: ==========================================
>>> TCL: == Init Variables
>>> TCL: ==========================================
>>> TCL: User selected BRAINS
>>> TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
>>>
>>>
>>> attemptToGoToNextStep - Attempting to go to the next step
>>> validateInternal - validating input from 6. Define Preprocessing
>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>> performTransitionBetweenSteps - Performing transition between steps
>>> onExitInternal - exiting 6. Define Preprocessing
>>>
>>> Traceback (most recent call last):
>>>      File "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py", line 121, in onExit
>>>        self.runPreProcessing()
>>>      File "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py", line 130, in runPreProcessing
>>>        message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while pre-processing runs..", qt.QMessageBox.Ignore )
>>> ValueError: Could not find matching overload for given arguments:
>>> (0, 'Please wait', 'Please wait while pre-processing 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)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ________________________________________
>>> From: Kilian Pohl [[hidden email]]
>>> Sent: Sunday, April 15, 2012 7:02 PM
>>> To: He,Renjie
>>> Subject: Re: EMsegmenter would not work
>>>
>>> Renje: One window could you do the following for me :
>>>
>>> after you get to the segment step where nothing is happening could you
>>> go to the top menu ->    View ->    Error Log ->    select each entry and copy
>>> /past the text in the frame below in this email. I know this is a little
>>> bit cumbersome but do not know how else to help you otherwise
>>>
>>> Steve: is there an easy way to get the log under Windows ?
>>>
>>>
>>> Thanks
>>>
>>> Kilian
>>>
>>> On 04/13/2012 05:07 PM, He,Renjie wrote:
>>>> Thanks! At least the Mac OS is working!
>>>>
>>>> ________________________________________
>>>> From: Kilian Pohl [[hidden email]]
>>>> Sent: Friday, April 13, 2012 4:03 PM
>>>> To: He,Renjie
>>>> Subject: Re: EMsegmenter would not work
>>>>
>>>> no - I will let you know in a little bit how to send me the log files
>>>>
>>>> K
>>>> On 4/13/2012 4:57 PM, He,Renjie wrote:
>>>>> All our Win systems are 32-bits, could this be the point?
>>>>>
>>>>> ________________________________________
>>>>> From: Kilian Pohl [[hidden email]]
>>>>> Sent: Friday, April 13, 2012 3:34 PM
>>>>> To: He,Renjie
>>>>> Subject: Re: EMsegmenter would not work
>>>>>
>>>>> I know that others are using the software and do not run into these
>>>>> problems. So if it happens to you then we have to dig a little bit
>>>>> deeper :)
>>>>>
>>>>> Kilian
>>>>>
>>>>>
>>>>> On 4/13/2012 4:23 PM, He,Renjie wrote:
>>>>>> Hi, Kilian,
>>>>>>
>>>>>> We did exactly what you mentioned! I will try it again on Mac OS and get back to you afterwards. Thanks!
>>>>>>
>>>>>> ________________________________________
>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>> Sent: Friday, April 13, 2012 3:16 PM
>>>>>> To: He,Renjie
>>>>>> Cc: Pohl, Kilian; Sonia Pujol
>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>
>>>>>> Slicer 3.6.3 is not supported . What tutorial did you use ?
>>>>>>
>>>>>> Could you do a simple test?
>>>>>>
>>>>>>         Load in an MR image, select the task MRI Human Brain in the
>>>>>> EMSegmenter and press the simple mode button. Then simply select the MR
>>>>>> scan you just loaded in and press segment. This should definitely work
>>>>>> on MAC with the 4.10. version. The other versions should be ignored.
>>>>>>
>>>>>> Once it works on a mac could you try it out on your windows machines  ?
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Kilian
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 4/13/2012 4:07 PM, He,Renjie wrote:
>>>>>>> Hi, Kilian,
>>>>>>>
>>>>>>> Thanks for the email! Our systems are:
>>>>>>>
>>>>>>> Desktop: Mac OS x 10.6 64-bit
>>>>>>>                        Win XP Pro 32-bit
>>>>>>>
>>>>>>> Laptop: Win Vista Home 32-bit
>>>>>>>
>>>>>>> we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the simple mode of EMsegment with altas according to the steps in the tutorial and the results are:
>>>>>>>
>>>>>>>
>>>>>>> 3.6.3: all gave the errors of scalar type mismatch
>>>>>>> 4.0.1: all failed to reponse the buttom of segment
>>>>>>> 4.1.0: all give the message "segmentation did not execute correctly!".
>>>>>>>
>>>>>>> Where could I find the log files?
>>>>>>>
>>>>>>> Thank again!
>>>>>>>
>>>>>>> Renjie
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: Pohl, Kilian [[hidden email]]
>>>>>>> Sent: Friday, April 13, 2012 2:52 PM
>>>>>>> To: He,Renjie; Sonia Pujol; [hidden email]
>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>
>>>>>>> Hi Renjie,
>>>>>>>
>>>>>>> What version of Slicer are you running, can you provide us with the log file, what operating system are you using (e.g. XP 64 bit) and what task are you executing ?
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Kilian
>>>>>>>
>>>>>>> Ps: Please send me responds back to [hidden email]
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: He,Renjie [mailto:[hidden email]]
>>>>>>> Sent: Fri 4/13/2012 2:04 PM
>>>>>>> To: Sonia Pujol
>>>>>>> Cc: Pohl, Kilian
>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>
>>>>>>> yes, it got the same message as "segmentation did not execute correctly!".
>>>>>>>
>>>>>>> ________________________________
>>>>>>> From: Sonia Pujol [[hidden email]]
>>>>>>> Sent: Friday, April 13, 2012 12:35 PM
>>>>>>> To: He,Renjie
>>>>>>> Cc: [hidden email]
>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>
>>>>>>> Hi Renjie,
>>>>>>>
>>>>>>> Which version of Slicer are you using ? I have cc-ed Kilian Polh who may have useful insights since he developed the EMSegmenter.
>>>>>>>
>>>>>>> Best Regards,
>>>>>>>
>>>>>>> Sonia
>>>>>>>
>>>>>>>
>>>>>>> On 4/13/12 12:49 PM, He,Renjie wrote:
>>>>>>> Dear Dr. Pujol,
>>>>>>>
>>>>>>> Sorry to bother you! We tried to make the EMsegmenter work but totally failed. On desktops (with Mac OS and Win XP), when click on the segment button, there is no response. On one laptop with Win Vista, the segmentation failed and get "segmentation did not execute correctly!". Could you please give us some hints, Many thanks!
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Renjie He
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Sonia Pujol, Ph.D.
>>>>>>> Surgical Planning Laboratory, Harvard Medical School
>>>>>>> Brigham and Women's Hospital, Boston, MA
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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Re: EMsegmenter would not work

Kilian Pohl
Does anybody know what it means if a module is in red color ?

K

-------- Original Message --------
Subject: RE: EMsegmenter would not work
Date: Thu, 26 Apr 2012 09:26:12 -0500
From: He,Renjie [hidden email]
To: Kilian Pohl [hidden email]


one more observation:

when I click Edit->Modules settings, I found "EMSegmenter with altas" is in red color, while all others are in black.

Renjie


On 4/26/2012 10:36 AM, Kilian Pohl wrote:
Hi Renjie,

On 4/26/2012 10:24 AM, He,Renjie wrote:
Dear Kilian,

I did all you mentioned, after run the simple segmentation on version 4.1.0, after a flash of altas on screen, it gives the same message: "segmentation did not execute correctly!".

The files generated during segmentation procedures are: pos files, aligned altas files, aligned t1 file, but deformVolume and EM_map are empty.
Are you running simple or advanced mode ? If you ran it in simple mode could you switch to advance mode and let me know exactly after which step you get an error message ?

Did you delete the directory ? Could you just send me the log that lists all the tasks that are added to the list similar to

[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
File :

...
in my previous email

Thanks

Kilian





Renjie


________________________________________
From: Kilian Pohl [[hidden email]]
Sent: Wednesday, April 25, 2012 6:56 PM
To: He,Renjie
Subject: Re: EMsegmenter would not work

Hi Renjie,

I assume you run into this problem when you run Slicer 4.1.0 and not
4.0.1- correct ? I just installed it on my machine and it runs fine .
One thing I noticed is that you have in

C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\

a couple of tasks that are not valid anymore . Could you do me a favour and remove the file

C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy

and restart Slicer as well as run the EMSegmenter ?

The directory should list the following mrml files :

[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
File :
'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
Full Parcellation'  File :
'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
Hemisphere'  File :
'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
Parcellation'  File :
'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
Brain'  File :
'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
[EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
Primate'  File :
'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
GetTclTaskDirectory::Copying task files ...
      from: D:/pieper/Slicer4.1/Slicer
4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
      to: C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy

Also do you mind if I post the next message on the slicer devel list so
that other can follow the track too ? Ron asked me to do that

Kilian


On 04/16/2012 06:06 PM, He,Renjie wrote:
Thanks for your attention!

________________________________________
From: Kilian Pohl [[hidden email]]
Sent: Monday, April 16, 2012 4:57 PM
To: He,Renjie
Subject: Re: EMsegmenter would not work

This helps a lot - I will further investigate next week

Kilian



On 4/16/2012 10:06 AM, He,Renjie wrote:
Dear Kilian,

Thank you so much for your time and help!

Here is the message for version 4.1.0 : "segmentation did not execute correctly!".
and log error:
ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line 2162
vtkEMSegmentLogic (1E2E6F10): Exception thrown during segmentation: bad allocation



Here is the log for version 4.0.1 :

Show module (name): "EMSegment"
onEntryInternal - entering input from 1. Define Task
processingAfterOnEntry
showUserInterface - showing 1. Define Task

GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy

[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand Bone'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human Eye'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion Exp'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Exp'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Full Parcellation'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Hemisphere'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain HIPR'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain Parcellation'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human Brain'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human Primate'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
[EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas Cluster'  File : 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy

goForward - posting ValidationTransition
attemptToGoToNextStep - Attempting to go to the next step
validateInternal - validating input from 1. Define Task

[EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI Human Brain' from file 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'

==========================================================================
== Completed importing data C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
==========================================================================
BiasCorrectionType: 0
UseLLS_Recompute_Means: 0
BiasCorrectionType: 0
UseLLS_Recompute_Means: 0
BiasCorrectionType: 0
UseLLS_Recompute_Means: 0
[EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy

goToNextStepAfterSuccessfulValidation - Calidation succeeded
goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
performTransitionBetweenSteps - Performing transition between steps
onExitInternal - exiting 1. Define Task
onEntryInternal - entering input from 2. Define Input Datasets
processingAfterOnEntry
updateClientArea - hiding 1. Define Task
showUserInterface - showing 2. Define Input Datasets

GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy

GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
Sourcing general Task file : C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
Sourcing task specific file: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl

goToStep - Attempting to go to finish step Segment
goForward - posting ValidationTransition
attemptToGoToNextStep - Attempting to go to the next step
validateInternal - validating input from 2. Define Input Datasets
goToNextStepAfterSuccessfulValidation - Calidation succeeded
goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
performTransitionBetweenSteps - Performing transition between steps
onExitInternal - exiting 2. Define Input Datasets
onEntryInternal - entering input from 3. Define Anatomical Tree
processingAfterOnEntry
goForward - posting ValidationTransition
attemptToGoToNextStep - Attempting to go to the next step
validateInternal - validating input from 3. Define Anatomical Tree
goToNextStepAfterSuccessfulValidation - Calidation succeeded
goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
performTransitionBetweenSteps - Performing transition between steps
onExitInternal - exiting 3. Define Anatomical Tree
onEntryInternal - entering input from 4. Define Atlas
processingAfterOnEntry
goForward - posting ValidationTransition
attemptToGoToNextStep - Attempting to go to the next step
validateInternal - validating input from 4. Define Atlas
goToNextStepAfterSuccessfulValidation - Calidation succeeded
goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
performTransitionBetweenSteps - Performing transition between steps
onExitInternal - exiting 4. Define Atlas
onEntryInternal - entering input from 5. Edit Registration Parameters
processingAfterOnEntry
goForward - posting ValidationTransition
attemptToGoToNextStep - Attempting to go to the next step
validateInternal - validating input from 5. Edit Registration Parameters
goToNextStepAfterSuccessfulValidation - Calidation succeeded
goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
performTransitionBetweenSteps - Performing transition between steps
onExitInternal - exiting 5. Edit Registration Parameters
onEntryInternal - entering input from 6. Define Preprocessing
processingAfterOnEntry
goForward - posting ValidationTransition


GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy

Sourcing general Task file : C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
Sourcing task specific file: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy

GetTclTaskDirectory::Copying task files ...
    from: C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
    to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
Sourcing general Task file : C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
Sourcing task specific file: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
couldn't read file "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl": no such file or directory
couldn't read file "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl": no such file or directory
       while executing
"source C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
TCL: ==========================================
TCL: == Init Variables
TCL: ==========================================
TCL: User selected BRAINS
TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface


attemptToGoToNextStep - Attempting to go to the next step
validateInternal - validating input from 6. Define Preprocessing
goToNextStepAfterSuccessfulValidation - Calidation succeeded
goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
performTransitionBetweenSteps - Performing transition between steps
onExitInternal - exiting 6. Define Preprocessing

Traceback (most recent call last):
     File "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py", line 121, in onExit
       self.runPreProcessing()
     File "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py", line 130, in runPreProcessing
       message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please wait", "Please wait while pre-processing runs..", qt.QMessageBox.Ignore )
ValueError: Could not find matching overload for given arguments:
(0, 'Please wait', 'Please wait while pre-processing 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)








________________________________________
From: Kilian Pohl [[hidden email]]
Sent: Sunday, April 15, 2012 7:02 PM
To: He,Renjie
Subject: Re: EMsegmenter would not work

Renje: One window could you do the following for me :

after you get to the segment step where nothing is happening could you
go to the top menu ->    View ->    Error Log ->    select each entry and copy
/past the text in the frame below in this email. I know this is a little
bit cumbersome but do not know how else to help you otherwise

Steve: is there an easy way to get the log under Windows ?


Thanks

Kilian

On 04/13/2012 05:07 PM, He,Renjie wrote:
Thanks! At least the Mac OS is working!

________________________________________
From: Kilian Pohl [[hidden email]]
Sent: Friday, April 13, 2012 4:03 PM
To: He,Renjie
Subject: Re: EMsegmenter would not work

no - I will let you know in a little bit how to send me the log files

K
On 4/13/2012 4:57 PM, He,Renjie wrote:
All our Win systems are 32-bits, could this be the point?

________________________________________
From: Kilian Pohl [[hidden email]]
Sent: Friday, April 13, 2012 3:34 PM
To: He,Renjie
Subject: Re: EMsegmenter would not work

I know that others are using the software and do not run into these
problems. So if it happens to you then we have to dig a little bit
deeper :)

Kilian


On 4/13/2012 4:23 PM, He,Renjie wrote:
Hi, Kilian,

We did exactly what you mentioned! I will try it again on Mac OS and get back to you afterwards. Thanks!

________________________________________
From: Kilian Pohl [[hidden email]]
Sent: Friday, April 13, 2012 3:16 PM
To: He,Renjie
Cc: Pohl, Kilian; Sonia Pujol
Subject: Re: EMsegmenter would not work

Slicer 3.6.3 is not supported . What tutorial did you use ?

Could you do a simple test?

        Load in an MR image, select the task MRI Human Brain in the
EMSegmenter and press the simple mode button. Then simply select the MR
scan you just loaded in and press segment. This should definitely work
on MAC with the 4.10. version. The other versions should be ignored.

Once it works on a mac could you try it out on your windows machines  ?

Thanks

Kilian



On 4/13/2012 4:07 PM, He,Renjie wrote:
Hi, Kilian,

Thanks for the email! Our systems are:

Desktop: Mac OS x 10.6 64-bit
                       Win XP Pro 32-bit

Laptop: Win Vista Home 32-bit

we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the simple mode of EMsegment with altas according to the steps in the tutorial and the results are:


3.6.3: all gave the errors of scalar type mismatch
4.0.1: all failed to reponse the buttom of segment
4.1.0: all give the message "segmentation did not execute correctly!".

Where could I find the log files?

Thank again!

Renjie




________________________________________
From: Pohl, Kilian [[hidden email]]
Sent: Friday, April 13, 2012 2:52 PM
To: He,Renjie; Sonia Pujol; [hidden email]
Subject: RE: EMsegmenter would not work

Hi Renjie,

What version of Slicer are you running, can you provide us with the log file, what operating system are you using (e.g. XP 64 bit) and what task are you executing ?

Thanks

Kilian

Ps: Please send me responds back to [hidden email]

-----Original Message-----
From: He,Renjie [[hidden email]]
Sent: Fri 4/13/2012 2:04 PM
To: Sonia Pujol
Cc: Pohl, Kilian
Subject: RE: EMsegmenter would not work

yes, it got the same message as "segmentation did not execute correctly!".

________________________________
From: Sonia Pujol [[hidden email]]
Sent: Friday, April 13, 2012 12:35 PM
To: He,Renjie
Cc: [hidden email]
Subject: Re: EMsegmenter would not work

Hi Renjie,

Which version of Slicer are you using ? I have cc-ed Kilian Polh who may have useful insights since he developed the EMSegmenter.

Best Regards,

Sonia


On 4/13/12 12:49 PM, He,Renjie wrote:
Dear Dr. Pujol,

Sorry to bother you! We tried to make the EMsegmenter work but totally failed. On desktops (with Mac OS and Win XP), when click on the segment button, there is no response. On one laptop with Win Vista, the segmentation failed and get "segmentation did not execute correctly!". Could you please give us some hints, Many thanks!

Best regards,
Renjie He



--
Sonia Pujol, Ph.D.
Surgical Planning Laboratory, Harvard Medical School
Brigham and Women's Hospital, Boston, MA



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Re: EMsegmenter would not work

Aucoin, Nicole
The module failed to load. When I start up slicer without CLI modules I
get this message in the terminal:
Loading module "CropVolume"
RegisterIO "qSlicerVolumesIO"
When loading module  "CropVolume" , the dependency
"ResampleScalarVectorDWIVolume" failed to be loaded.

and in Edit -> Application Settings -> Module Settings, CropVolume is in
red.

Nicole

On 04/26/2012 10:38 AM, Kilian Pohl wrote:

> Does anybody know what it means if a module is in red color ?
>
> K
>
> -------- Original Message --------
> Subject: RE: EMsegmenter would not work
> Date: Thu, 26 Apr 2012 09:26:12 -0500
> From: He,Renjie <[hidden email]>
> To: Kilian Pohl <[hidden email]>
>
>
>
> one more observation:
>
> when I click Edit->Modules settings, I found "EMSegmenter with altas" is in red color, while all others are in black.
>
> Renjie
>
>
> On 4/26/2012 10:36 AM, Kilian Pohl wrote:
>> Hi Renjie,
>>
>> On 4/26/2012 10:24 AM, He,Renjie wrote:
>>> Dear Kilian,
>>>
>>> I did all you mentioned, after run the simple segmentation on
>>> version 4.1.0, after a flash of altas on screen, it gives the same
>>> message: "segmentation did not execute correctly!".
>>>
>>> The files generated during segmentation procedures are: pos files,
>>> aligned altas files, aligned t1 file, but deformVolume and EM_map
>>> are empty.
>> Are you running simple or advanced mode ? If you ran it in simple
>> mode could you switch to advance mode and let me know exactly after
>> which step you get an error message ?
>>
>> Did you delete the directory ? Could you just send me the log that
>> lists all the tasks that are added to the list similar to
>>
>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>> File :
>>
>> ...
>> in my previous email
>>
>> Thanks
>>
>> Kilian
>>
>>
>>
>>
>>>
>>> Renjie
>>>
>>>
>>> ________________________________________
>>> From: Kilian Pohl [[hidden email]]
>>> Sent: Wednesday, April 25, 2012 6:56 PM
>>> To: He,Renjie
>>> Subject: Re: EMsegmenter would not work
>>>
>>> Hi Renjie,
>>>
>>> I assume you run into this problem when you run Slicer 4.1.0 and not
>>> 4.0.1- correct ? I just installed it on my machine and it runs fine .
>>> One thing I noticed is that you have in
>>>
>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\
>>>
>>> a couple of tasks that are not valid anymore . Could you do me a
>>> favour and remove the file
>>>
>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy
>>>
>>> and restart Slicer as well as run the EMSegmenter ?
>>>
>>> The directory should list the following mrml files :
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>> File :
>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>> Full Parcellation'  File :
>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>> Hemisphere'  File :
>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>> Parcellation'  File :
>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
>>> Brain'  File :
>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
>>> Primate'  File :
>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>
>>> GetTclTaskDirectory::Copying task files ...
>>>       from: D:/pieper/Slicer4.1/Slicer
>>> 4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
>>>       to:
>>> C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy
>>>
>>> Also do you mind if I post the next message on the slicer devel list so
>>> that other can follow the track too ? Ron asked me to do that
>>>
>>> Kilian
>>>
>>>
>>> On 04/16/2012 06:06 PM, He,Renjie wrote:
>>>> Thanks for your attention!
>>>>
>>>> ________________________________________
>>>> From: Kilian Pohl [[hidden email]]
>>>> Sent: Monday, April 16, 2012 4:57 PM
>>>> To: He,Renjie
>>>> Subject: Re: EMsegmenter would not work
>>>>
>>>> This helps a lot - I will further investigate next week
>>>>
>>>> Kilian
>>>>
>>>>
>>>>
>>>> On 4/16/2012 10:06 AM, He,Renjie wrote:
>>>>> Dear Kilian,
>>>>>
>>>>> Thank you so much for your time and help!
>>>>>
>>>>> Here is the message for version 4.1.0 : "segmentation did not
>>>>> execute correctly!".
>>>>> and log error:
>>>>> ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line
>>>>> 2162
>>>>> vtkEMSegmentLogic (1E2E6F10): Exception thrown during
>>>>> segmentation: bad allocation
>>>>>
>>>>>
>>>>>
>>>>> Here is the log for version 4.0.1 :
>>>>>
>>>>> Show module (name): "EMSegment"
>>>>> onEntryInternal - entering input from 1. Define Task
>>>>> processingAfterOnEntry
>>>>> showUserInterface - showing 1. Define Task
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand
>>>>> Bone'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human
>>>>> Eye'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
>>>>>
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion
>>>>> Exp'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>> Brain Exp'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>> Brain Full Parcellation'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>> Brain Hemisphere'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>> Brain HIPR'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>> Brain Parcellation'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>> Brain'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human
>>>>> Primate'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas
>>>>> Cluster'  File :
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> goForward - posting ValidationTransition
>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>> validateInternal - validating input from 1. Define Task
>>>>>
>>>>> [EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI
>>>>> Human Brain' from file
>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>
>>>>> ==========================================================================
>>>>>
>>>>> == Completed importing data
>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
>>>>> ==========================================================================
>>>>>
>>>>> BiasCorrectionType: 0
>>>>> UseLLS_Recompute_Means: 0
>>>>> BiasCorrectionType: 0
>>>>> UseLLS_Recompute_Means: 0
>>>>> BiasCorrectionType: 0
>>>>> UseLLS_Recompute_Means: 0
>>>>> [EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>> onExitInternal - exiting 1. Define Task
>>>>> onEntryInternal - entering input from 2. Define Input Datasets
>>>>> processingAfterOnEntry
>>>>> updateClientArea - hiding 1. Define Task
>>>>> showUserInterface - showing 2. Define Input Datasets
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>> Sourcing general Task file :
>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>
>>>>> Sourcing task specific file:
>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>
>>>>> goToStep - Attempting to go to finish step Segment
>>>>> goForward - posting ValidationTransition
>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>> validateInternal - validating input from 2. Define Input Datasets
>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>> onExitInternal - exiting 2. Define Input Datasets
>>>>> onEntryInternal - entering input from 3. Define Anatomical Tree
>>>>> processingAfterOnEntry
>>>>> goForward - posting ValidationTransition
>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>> validateInternal - validating input from 3. Define Anatomical Tree
>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>> onExitInternal - exiting 3. Define Anatomical Tree
>>>>> onEntryInternal - entering input from 4. Define Atlas
>>>>> processingAfterOnEntry
>>>>> goForward - posting ValidationTransition
>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>> validateInternal - validating input from 4. Define Atlas
>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>> onExitInternal - exiting 4. Define Atlas
>>>>> onEntryInternal - entering input from 5. Edit Registration Parameters
>>>>> processingAfterOnEntry
>>>>> goForward - posting ValidationTransition
>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>> validateInternal - validating input from 5. Edit Registration
>>>>> Parameters
>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>> onExitInternal - exiting 5. Edit Registration Parameters
>>>>> onEntryInternal - entering input from 6. Define Preprocessing
>>>>> processingAfterOnEntry
>>>>> goForward - posting ValidationTransition
>>>>>
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> Sourcing general Task file :
>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>
>>>>> Sourcing task specific file:
>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>     from:
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>> Sourcing general Task file :
>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>
>>>>> Sourcing task specific file:
>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>> couldn't read file
>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>> no such file or directory
>>>>> couldn't read file
>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>> no such file or directory
>>>>>        while executing
>>>>> "source
>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
>>>>> TCL: ==========================================
>>>>> TCL: == Init Variables
>>>>> TCL: ==========================================
>>>>> TCL: User selected BRAINS
>>>>> TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
>>>>>
>>>>>
>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>> validateInternal - validating input from 6. Define Preprocessing
>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>> onExitInternal - exiting 6. Define Preprocessing
>>>>>
>>>>> Traceback (most recent call last):
>>>>>      File
>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>> line 121, in onExit
>>>>>        self.runPreProcessing()
>>>>>      File
>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>> line 130, in runPreProcessing
>>>>>        message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please
>>>>> wait", "Please wait while pre-processing runs..",
>>>>> qt.QMessageBox.Ignore )
>>>>> ValueError: Could not find matching overload for given arguments:
>>>>> (0, 'Please wait', 'Please wait while pre-processing 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)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: Kilian Pohl [[hidden email]]
>>>>> Sent: Sunday, April 15, 2012 7:02 PM
>>>>> To: He,Renjie
>>>>> Subject: Re: EMsegmenter would not work
>>>>>
>>>>> Renje: One window could you do the following for me :
>>>>>
>>>>> after you get to the segment step where nothing is happening could
>>>>> you
>>>>> go to the top menu ->    View ->    Error Log ->    select each
>>>>> entry and copy
>>>>> /past the text in the frame below in this email. I know this is a
>>>>> little
>>>>> bit cumbersome but do not know how else to help you otherwise
>>>>>
>>>>> Steve: is there an easy way to get the log under Windows ?
>>>>>
>>>>>
>>>>> Thanks
>>>>>
>>>>> Kilian
>>>>>
>>>>> On 04/13/2012 05:07 PM, He,Renjie wrote:
>>>>>> Thanks! At least the Mac OS is working!
>>>>>>
>>>>>> ________________________________________
>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>> Sent: Friday, April 13, 2012 4:03 PM
>>>>>> To: He,Renjie
>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>
>>>>>> no - I will let you know in a little bit how to send me the log
>>>>>> files
>>>>>>
>>>>>> K
>>>>>> On 4/13/2012 4:57 PM, He,Renjie wrote:
>>>>>>> All our Win systems are 32-bits, could this be the point?
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>> Sent: Friday, April 13, 2012 3:34 PM
>>>>>>> To: He,Renjie
>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>
>>>>>>> I know that others are using the software and do not run into these
>>>>>>> problems. So if it happens to you then we have to dig a little bit
>>>>>>> deeper :)
>>>>>>>
>>>>>>> Kilian
>>>>>>>
>>>>>>>
>>>>>>> On 4/13/2012 4:23 PM, He,Renjie wrote:
>>>>>>>> Hi, Kilian,
>>>>>>>>
>>>>>>>> We did exactly what you mentioned! I will try it again on Mac
>>>>>>>> OS and get back to you afterwards. Thanks!
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>> Sent: Friday, April 13, 2012 3:16 PM
>>>>>>>> To: He,Renjie
>>>>>>>> Cc: Pohl, Kilian; Sonia Pujol
>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>
>>>>>>>> Slicer 3.6.3 is not supported . What tutorial did you use ?
>>>>>>>>
>>>>>>>> Could you do a simple test?
>>>>>>>>
>>>>>>>>         Load in an MR image, select the task MRI Human Brain in
>>>>>>>> the
>>>>>>>> EMSegmenter and press the simple mode button. Then simply
>>>>>>>> select the MR
>>>>>>>> scan you just loaded in and press segment. This should
>>>>>>>> definitely work
>>>>>>>> on MAC with the 4.10. version. The other versions should be
>>>>>>>> ignored.
>>>>>>>>
>>>>>>>> Once it works on a mac could you try it out on your windows
>>>>>>>> machines  ?
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Kilian
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 4/13/2012 4:07 PM, He,Renjie wrote:
>>>>>>>>> Hi, Kilian,
>>>>>>>>>
>>>>>>>>> Thanks for the email! Our systems are:
>>>>>>>>>
>>>>>>>>> Desktop: Mac OS x 10.6 64-bit
>>>>>>>>>                        Win XP Pro 32-bit
>>>>>>>>>
>>>>>>>>> Laptop: Win Vista Home 32-bit
>>>>>>>>>
>>>>>>>>> we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the
>>>>>>>>> simple mode of EMsegment with altas according to the steps in
>>>>>>>>> the tutorial and the results are:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 3.6.3: all gave the errors of scalar type mismatch
>>>>>>>>> 4.0.1: all failed to reponse the buttom of segment
>>>>>>>>> 4.1.0: all give the message "segmentation did not execute
>>>>>>>>> correctly!".
>>>>>>>>>
>>>>>>>>> Where could I find the log files?
>>>>>>>>>
>>>>>>>>> Thank again!
>>>>>>>>>
>>>>>>>>> Renjie
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ________________________________________
>>>>>>>>> From: Pohl, Kilian [[hidden email]]
>>>>>>>>> Sent: Friday, April 13, 2012 2:52 PM
>>>>>>>>> To: He,Renjie; Sonia Pujol; [hidden email]
>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> Hi Renjie,
>>>>>>>>>
>>>>>>>>> What version of Slicer are you running, can you provide us
>>>>>>>>> with the log file, what operating system are you using (e.g.
>>>>>>>>> XP 64 bit) and what task are you executing ?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Kilian
>>>>>>>>>
>>>>>>>>> Ps: Please send me responds back to [hidden email]
>>>>>>>>>
>>>>>>>>> -----Original Message-----
>>>>>>>>> From: He,Renjie [mailto:[hidden email]]
>>>>>>>>> Sent: Fri 4/13/2012 2:04 PM
>>>>>>>>> To: Sonia Pujol
>>>>>>>>> Cc: Pohl, Kilian
>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> yes, it got the same message as "segmentation did not execute
>>>>>>>>> correctly!".
>>>>>>>>>
>>>>>>>>> ________________________________
>>>>>>>>> From: Sonia Pujol [[hidden email]]
>>>>>>>>> Sent: Friday, April 13, 2012 12:35 PM
>>>>>>>>> To: He,Renjie
>>>>>>>>> Cc: [hidden email]
>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> Hi Renjie,
>>>>>>>>>
>>>>>>>>> Which version of Slicer are you using ? I have cc-ed Kilian
>>>>>>>>> Polh who may have useful insights since he developed the
>>>>>>>>> EMSegmenter.
>>>>>>>>>
>>>>>>>>> Best Regards,
>>>>>>>>>
>>>>>>>>> Sonia
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/13/12 12:49 PM, He,Renjie wrote:
>>>>>>>>> Dear Dr. Pujol,
>>>>>>>>>
>>>>>>>>> Sorry to bother you! We tried to make the EMsegmenter work but
>>>>>>>>> totally failed. On desktops (with Mac OS and Win XP), when
>>>>>>>>> click on the segment button, there is no response. On one
>>>>>>>>> laptop with Win Vista, the segmentation failed and get
>>>>>>>>> "segmentation did not execute correctly!". Could you please
>>>>>>>>> give us some hints, Many thanks!
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>> Renjie He
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Sonia Pujol, Ph.D.
>>>>>>>>> Surgical Planning Laboratory, Harvard Medical School
>>>>>>>>> Brigham and Women's Hospital, Boston, MA
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The information contained in this e-mail message is intended
>>>>>>>>> only for the personal and confidential use of the recipient(s)
>>>>>>>>> named above. If the reader of this message is not the intended
>>>>>>>>> recipient or an agent responsible for delivering it to the
>>>>>>>>> intended recipient, you are hereby notified that you have
>>>>>>>>> received this document in error and that any review,
>>>>>>>>> dissemination, distribution, or copying of this message is
>>>>>>>>> strictly prohibited. If you have received this communication
>>>>>>>>> in error, please notify us immediately by e-mail, and delete
>>>>>>>>> the original message.
>>
>
>
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Re: EMsegmenter would not work

Andrey Fedorov
On Thu, Apr 26, 2012 at 10:54 AM, Nicole Aucoin <[hidden email]> wrote:
> The module failed to load. When I start up slicer without CLI modules I
> get this message in the terminal:
> Loading module "CropVolume"
> RegisterIO "qSlicerVolumesIO"
> When loading module  "CropVolume" , the dependency
> "ResampleScalarVectorDWIVolume" failed to be loaded.
>

I wonder if it makes sense to add a popup warning window to notify the
users when a dependency fails for a selected module.

In my opinion, it would make more sense not to load modules with
failed dependencies at all.

> and in Edit -> Application Settings -> Module Settings, CropVolume is in
> red.
>
> Nicole
>
> On 04/26/2012 10:38 AM, Kilian Pohl wrote:
>> Does anybody know what it means if a module is in red color ?
>>
>> K
>>
>> -------- Original Message --------
>> Subject:      RE: EMsegmenter would not work
>> Date:         Thu, 26 Apr 2012 09:26:12 -0500
>> From:         He,Renjie <[hidden email]>
>> To:   Kilian Pohl <[hidden email]>
>>
>>
>>
>> one more observation:
>>
>> when I click Edit->Modules settings, I found "EMSegmenter with altas" is in red color, while all others are in black.
>>
>> Renjie
>>
>>
>> On 4/26/2012 10:36 AM, Kilian Pohl wrote:
>>> Hi Renjie,
>>>
>>> On 4/26/2012 10:24 AM, He,Renjie wrote:
>>>> Dear Kilian,
>>>>
>>>> I did all you mentioned, after run the simple segmentation on
>>>> version 4.1.0, after a flash of altas on screen, it gives the same
>>>> message: "segmentation did not execute correctly!".
>>>>
>>>> The files generated during segmentation procedures are: pos files,
>>>> aligned altas files, aligned t1 file, but deformVolume and EM_map
>>>> are empty.
>>> Are you running simple or advanced mode ? If you ran it in simple
>>> mode could you switch to advance mode and let me know exactly after
>>> which step you get an error message ?
>>>
>>> Did you delete the directory ? Could you just send me the log that
>>> lists all the tasks that are added to the list similar to
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>> File :
>>>
>>> ...
>>> in my previous email
>>>
>>> Thanks
>>>
>>> Kilian
>>>
>>>
>>>
>>>
>>>>
>>>> Renjie
>>>>
>>>>
>>>> ________________________________________
>>>> From: Kilian Pohl [[hidden email]]
>>>> Sent: Wednesday, April 25, 2012 6:56 PM
>>>> To: He,Renjie
>>>> Subject: Re: EMsegmenter would not work
>>>>
>>>> Hi Renjie,
>>>>
>>>> I assume you run into this problem when you run Slicer 4.1.0 and not
>>>> 4.0.1- correct ? I just installed it on my machine and it runs fine .
>>>> One thing I noticed is that you have in
>>>>
>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\
>>>>
>>>> a couple of tasks that are not valid anymore . Could you do me a
>>>> favour and remove the file
>>>>
>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy
>>>>
>>>> and restart Slicer as well as run the EMSegmenter ?
>>>>
>>>> The directory should list the following mrml files :
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>>> File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>> Full Parcellation'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>> Hemisphere'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>> Parcellation'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
>>>> Brain'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
>>>> Primate'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>
>>>> GetTclTaskDirectory::Copying task files ...
>>>>       from: D:/pieper/Slicer4.1/Slicer
>>>> 4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
>>>>       to:
>>>> C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy
>>>>
>>>> Also do you mind if I post the next message on the slicer devel list so
>>>> that other can follow the track too ? Ron asked me to do that
>>>>
>>>> Kilian
>>>>
>>>>
>>>> On 04/16/2012 06:06 PM, He,Renjie wrote:
>>>>> Thanks for your attention!
>>>>>
>>>>> ________________________________________
>>>>> From: Kilian Pohl [[hidden email]]
>>>>> Sent: Monday, April 16, 2012 4:57 PM
>>>>> To: He,Renjie
>>>>> Subject: Re: EMsegmenter would not work
>>>>>
>>>>> This helps a lot - I will further investigate next week
>>>>>
>>>>> Kilian
>>>>>
>>>>>
>>>>>
>>>>> On 4/16/2012 10:06 AM, He,Renjie wrote:
>>>>>> Dear Kilian,
>>>>>>
>>>>>> Thank you so much for your time and help!
>>>>>>
>>>>>> Here is the message for version 4.1.0 : "segmentation did not
>>>>>> execute correctly!".
>>>>>> and log error:
>>>>>> ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line
>>>>>> 2162
>>>>>> vtkEMSegmentLogic (1E2E6F10): Exception thrown during
>>>>>> segmentation: bad allocation
>>>>>>
>>>>>>
>>>>>>
>>>>>> Here is the log for version 4.0.1 :
>>>>>>
>>>>>> Show module (name): "EMSegment"
>>>>>> onEntryInternal - entering input from 1. Define Task
>>>>>> processingAfterOnEntry
>>>>>> showUserInterface - showing 1. Define Task
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand
>>>>>> Bone'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human
>>>>>> Eye'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
>>>>>>
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion
>>>>>> Exp'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Exp'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Full Parcellation'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Hemisphere'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain HIPR'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Parcellation'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human
>>>>>> Primate'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas
>>>>>> Cluster'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 1. Define Task
>>>>>>
>>>>>> [EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI
>>>>>> Human Brain' from file
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>>
>>>>>> ==========================================================================
>>>>>>
>>>>>> == Completed importing data
>>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
>>>>>> ==========================================================================
>>>>>>
>>>>>> BiasCorrectionType: 0
>>>>>> UseLLS_Recompute_Means: 0
>>>>>> BiasCorrectionType: 0
>>>>>> UseLLS_Recompute_Means: 0
>>>>>> BiasCorrectionType: 0
>>>>>> UseLLS_Recompute_Means: 0
>>>>>> [EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 1. Define Task
>>>>>> onEntryInternal - entering input from 2. Define Input Datasets
>>>>>> processingAfterOnEntry
>>>>>> updateClientArea - hiding 1. Define Task
>>>>>> showUserInterface - showing 2. Define Input Datasets
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>> Sourcing general Task file :
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>
>>>>>> Sourcing task specific file:
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>
>>>>>> goToStep - Attempting to go to finish step Segment
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 2. Define Input Datasets
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 2. Define Input Datasets
>>>>>> onEntryInternal - entering input from 3. Define Anatomical Tree
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 3. Define Anatomical Tree
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 3. Define Anatomical Tree
>>>>>> onEntryInternal - entering input from 4. Define Atlas
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 4. Define Atlas
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 4. Define Atlas
>>>>>> onEntryInternal - entering input from 5. Edit Registration Parameters
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 5. Edit Registration
>>>>>> Parameters
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 5. Edit Registration Parameters
>>>>>> onEntryInternal - entering input from 6. Define Preprocessing
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>>
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> Sourcing general Task file :
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>
>>>>>> Sourcing task specific file:
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>> Sourcing general Task file :
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>
>>>>>> Sourcing task specific file:
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>> couldn't read file
>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>> no such file or directory
>>>>>> couldn't read file
>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>> no such file or directory
>>>>>>        while executing
>>>>>> "source
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
>>>>>> TCL: ==========================================
>>>>>> TCL: == Init Variables
>>>>>> TCL: ==========================================
>>>>>> TCL: User selected BRAINS
>>>>>> TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
>>>>>>
>>>>>>
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 6. Define Preprocessing
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 6. Define Preprocessing
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>      File
>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>> line 121, in onExit
>>>>>>        self.runPreProcessing()
>>>>>>      File
>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>> line 130, in runPreProcessing
>>>>>>        message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please
>>>>>> wait", "Please wait while pre-processing runs..",
>>>>>> qt.QMessageBox.Ignore )
>>>>>> ValueError: Could not find matching overload for given arguments:
>>>>>> (0, 'Please wait', 'Please wait while pre-processing 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)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ________________________________________
>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>> Sent: Sunday, April 15, 2012 7:02 PM
>>>>>> To: He,Renjie
>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>
>>>>>> Renje: One window could you do the following for me :
>>>>>>
>>>>>> after you get to the segment step where nothing is happening could
>>>>>> you
>>>>>> go to the top menu ->    View ->    Error Log ->    select each
>>>>>> entry and copy
>>>>>> /past the text in the frame below in this email. I know this is a
>>>>>> little
>>>>>> bit cumbersome but do not know how else to help you otherwise
>>>>>>
>>>>>> Steve: is there an easy way to get the log under Windows ?
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Kilian
>>>>>>
>>>>>> On 04/13/2012 05:07 PM, He,Renjie wrote:
>>>>>>> Thanks! At least the Mac OS is working!
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>> Sent: Friday, April 13, 2012 4:03 PM
>>>>>>> To: He,Renjie
>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>
>>>>>>> no - I will let you know in a little bit how to send me the log
>>>>>>> files
>>>>>>>
>>>>>>> K
>>>>>>> On 4/13/2012 4:57 PM, He,Renjie wrote:
>>>>>>>> All our Win systems are 32-bits, could this be the point?
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>> Sent: Friday, April 13, 2012 3:34 PM
>>>>>>>> To: He,Renjie
>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>
>>>>>>>> I know that others are using the software and do not run into these
>>>>>>>> problems. So if it happens to you then we have to dig a little bit
>>>>>>>> deeper :)
>>>>>>>>
>>>>>>>> Kilian
>>>>>>>>
>>>>>>>>
>>>>>>>> On 4/13/2012 4:23 PM, He,Renjie wrote:
>>>>>>>>> Hi, Kilian,
>>>>>>>>>
>>>>>>>>> We did exactly what you mentioned! I will try it again on Mac
>>>>>>>>> OS and get back to you afterwards. Thanks!
>>>>>>>>>
>>>>>>>>> ________________________________________
>>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>>> Sent: Friday, April 13, 2012 3:16 PM
>>>>>>>>> To: He,Renjie
>>>>>>>>> Cc: Pohl, Kilian; Sonia Pujol
>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> Slicer 3.6.3 is not supported . What tutorial did you use ?
>>>>>>>>>
>>>>>>>>> Could you do a simple test?
>>>>>>>>>
>>>>>>>>>         Load in an MR image, select the task MRI Human Brain in
>>>>>>>>> the
>>>>>>>>> EMSegmenter and press the simple mode button. Then simply
>>>>>>>>> select the MR
>>>>>>>>> scan you just loaded in and press segment. This should
>>>>>>>>> definitely work
>>>>>>>>> on MAC with the 4.10. version. The other versions should be
>>>>>>>>> ignored.
>>>>>>>>>
>>>>>>>>> Once it works on a mac could you try it out on your windows
>>>>>>>>> machines  ?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Kilian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/13/2012 4:07 PM, He,Renjie wrote:
>>>>>>>>>> Hi, Kilian,
>>>>>>>>>>
>>>>>>>>>> Thanks for the email! Our systems are:
>>>>>>>>>>
>>>>>>>>>> Desktop: Mac OS x 10.6 64-bit
>>>>>>>>>>                        Win XP Pro 32-bit
>>>>>>>>>>
>>>>>>>>>> Laptop: Win Vista Home 32-bit
>>>>>>>>>>
>>>>>>>>>> we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the
>>>>>>>>>> simple mode of EMsegment with altas according to the steps in
>>>>>>>>>> the tutorial and the results are:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 3.6.3: all gave the errors of scalar type mismatch
>>>>>>>>>> 4.0.1: all failed to reponse the buttom of segment
>>>>>>>>>> 4.1.0: all give the message "segmentation did not execute
>>>>>>>>>> correctly!".
>>>>>>>>>>
>>>>>>>>>> Where could I find the log files?
>>>>>>>>>>
>>>>>>>>>> Thank again!
>>>>>>>>>>
>>>>>>>>>> Renjie
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ________________________________________
>>>>>>>>>> From: Pohl, Kilian [[hidden email]]
>>>>>>>>>> Sent: Friday, April 13, 2012 2:52 PM
>>>>>>>>>> To: He,Renjie; Sonia Pujol; [hidden email]
>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> Hi Renjie,
>>>>>>>>>>
>>>>>>>>>> What version of Slicer are you running, can you provide us
>>>>>>>>>> with the log file, what operating system are you using (e.g.
>>>>>>>>>> XP 64 bit) and what task are you executing ?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Kilian
>>>>>>>>>>
>>>>>>>>>> Ps: Please send me responds back to [hidden email]
>>>>>>>>>>
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: He,Renjie [mailto:[hidden email]]
>>>>>>>>>> Sent: Fri 4/13/2012 2:04 PM
>>>>>>>>>> To: Sonia Pujol
>>>>>>>>>> Cc: Pohl, Kilian
>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> yes, it got the same message as "segmentation did not execute
>>>>>>>>>> correctly!".
>>>>>>>>>>
>>>>>>>>>> ________________________________
>>>>>>>>>> From: Sonia Pujol [[hidden email]]
>>>>>>>>>> Sent: Friday, April 13, 2012 12:35 PM
>>>>>>>>>> To: He,Renjie
>>>>>>>>>> Cc: [hidden email]
>>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> Hi Renjie,
>>>>>>>>>>
>>>>>>>>>> Which version of Slicer are you using ? I have cc-ed Kilian
>>>>>>>>>> Polh who may have useful insights since he developed the
>>>>>>>>>> EMSegmenter.
>>>>>>>>>>
>>>>>>>>>> Best Regards,
>>>>>>>>>>
>>>>>>>>>> Sonia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 4/13/12 12:49 PM, He,Renjie wrote:
>>>>>>>>>> Dear Dr. Pujol,
>>>>>>>>>>
>>>>>>>>>> Sorry to bother you! We tried to make the EMsegmenter work but
>>>>>>>>>> totally failed. On desktops (with Mac OS and Win XP), when
>>>>>>>>>> click on the segment button, there is no response. On one
>>>>>>>>>> laptop with Win Vista, the segmentation failed and get
>>>>>>>>>> "segmentation did not execute correctly!". Could you please
>>>>>>>>>> give us some hints, Many thanks!
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>> Renjie He
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Sonia Pujol, Ph.D.
>>>>>>>>>> Surgical Planning Laboratory, Harvard Medical School
>>>>>>>>>> Brigham and Women's Hospital, Boston, MA
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The information contained in this e-mail message is intended
>>>>>>>>>> only for the personal and confidential use of the recipient(s)
>>>>>>>>>> named above. If the reader of this message is not the intended
>>>>>>>>>> recipient or an agent responsible for delivering it to the
>>>>>>>>>> intended recipient, you are hereby notified that you have
>>>>>>>>>> received this document in error and that any review,
>>>>>>>>>> dissemination, distribution, or copying of this message is
>>>>>>>>>> strictly prohibited. If you have received this communication
>>>>>>>>>> in error, please notify us immediately by e-mail, and delete
>>>>>>>>>> the original message.
>>>
>>
>>
>> _______________________________________________
>> 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: EMsegmenter would not work

Kilian Pohl
is there an easy way for Renjie to find out which dependencies failed ?

Kilian
On 4/26/2012 11:00 AM, Andriy Fedorov wrote:

> On Thu, Apr 26, 2012 at 10:54 AM, Nicole Aucoin<[hidden email]>  wrote:
>> The module failed to load. When I start up slicer without CLI modules I
>> get this message in the terminal:
>> Loading module "CropVolume"
>> RegisterIO "qSlicerVolumesIO"
>> When loading module  "CropVolume" , the dependency
>> "ResampleScalarVectorDWIVolume" failed to be loaded.
>>
> I wonder if it makes sense to add a popup warning window to notify the
> users when a dependency fails for a selected module.
>
> In my opinion, it would make more sense not to load modules with
> failed dependencies at all.
>
>> and in Edit ->  Application Settings ->  Module Settings, CropVolume is in
>> red.
>>
>> Nicole
>>
>> On 04/26/2012 10:38 AM, Kilian Pohl wrote:
>>> Does anybody know what it means if a module is in red color ?
>>>
>>> K
>>>
>>> -------- Original Message --------
>>> Subject:      RE: EMsegmenter would not work
>>> Date:         Thu, 26 Apr 2012 09:26:12 -0500
>>> From:         He,Renjie<[hidden email]>
>>> To:   Kilian Pohl<[hidden email]>
>>>
>>>
>>>
>>> one more observation:
>>>
>>> when I click Edit->Modules settings, I found "EMSegmenter with altas" is in red color, while all others are in black.
>>>
>>> Renjie
>>>
>>>
>>> On 4/26/2012 10:36 AM, Kilian Pohl wrote:
>>>> Hi Renjie,
>>>>
>>>> On 4/26/2012 10:24 AM, He,Renjie wrote:
>>>>> Dear Kilian,
>>>>>
>>>>> I did all you mentioned, after run the simple segmentation on
>>>>> version 4.1.0, after a flash of altas on screen, it gives the same
>>>>> message: "segmentation did not execute correctly!".
>>>>>
>>>>> The files generated during segmentation procedures are: pos files,
>>>>> aligned altas files, aligned t1 file, but deformVolume and EM_map
>>>>> are empty.
>>>> Are you running simple or advanced mode ? If you ran it in simple
>>>> mode could you switch to advance mode and let me know exactly after
>>>> which step you get an error message ?
>>>>
>>>> Did you delete the directory ? Could you just send me the log that
>>>> lists all the tasks that are added to the list similar to
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>>> File :
>>>>
>>>> ...
>>>> in my previous email
>>>>
>>>> Thanks
>>>>
>>>> Kilian
>>>>
>>>>
>>>>
>>>>
>>>>> Renjie
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: Kilian Pohl [[hidden email]]
>>>>> Sent: Wednesday, April 25, 2012 6:56 PM
>>>>> To: He,Renjie
>>>>> Subject: Re: EMsegmenter would not work
>>>>>
>>>>> Hi Renjie,
>>>>>
>>>>> I assume you run into this problem when you run Slicer 4.1.0 and not
>>>>> 4.0.1- correct ? I just installed it on my machine and it runs fine .
>>>>> One thing I noticed is that you have in
>>>>>
>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\
>>>>>
>>>>> a couple of tasks that are not valid anymore . Could you do me a
>>>>> favour and remove the file
>>>>>
>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy
>>>>>
>>>>> and restart Slicer as well as run the EMSegmenter ?
>>>>>
>>>>> The directory should list the following mrml files :
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>>>> File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>>> Full Parcellation'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>>> Hemisphere'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>>> Parcellation'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
>>>>> Brain'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
>>>>> Primate'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>        from: D:/pieper/Slicer4.1/Slicer
>>>>> 4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
>>>>>        to:
>>>>> C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> Also do you mind if I post the next message on the slicer devel list so
>>>>> that other can follow the track too ? Ron asked me to do that
>>>>>
>>>>> Kilian
>>>>>
>>>>>
>>>>> On 04/16/2012 06:06 PM, He,Renjie wrote:
>>>>>> Thanks for your attention!
>>>>>>
>>>>>> ________________________________________
>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>> Sent: Monday, April 16, 2012 4:57 PM
>>>>>> To: He,Renjie
>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>
>>>>>> This helps a lot - I will further investigate next week
>>>>>>
>>>>>> Kilian
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 4/16/2012 10:06 AM, He,Renjie wrote:
>>>>>>> Dear Kilian,
>>>>>>>
>>>>>>> Thank you so much for your time and help!
>>>>>>>
>>>>>>> Here is the message for version 4.1.0 : "segmentation did not
>>>>>>> execute correctly!".
>>>>>>> and log error:
>>>>>>> ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line
>>>>>>> 2162
>>>>>>> vtkEMSegmentLogic (1E2E6F10): Exception thrown during
>>>>>>> segmentation: bad allocation
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Here is the log for version 4.0.1 :
>>>>>>>
>>>>>>> Show module (name): "EMSegment"
>>>>>>> onEntryInternal - entering input from 1. Define Task
>>>>>>> processingAfterOnEntry
>>>>>>> showUserInterface - showing 1. Define Task
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand
>>>>>>> Bone'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human
>>>>>>> Eye'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
>>>>>>>
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion
>>>>>>> Exp'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Exp'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Full Parcellation'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Hemisphere'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain HIPR'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Parcellation'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human
>>>>>>> Primate'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas
>>>>>>> Cluster'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 1. Define Task
>>>>>>>
>>>>>>> [EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI
>>>>>>> Human Brain' from file
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>>>
>>>>>>> ==========================================================================
>>>>>>>
>>>>>>> == Completed importing data
>>>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
>>>>>>> ==========================================================================
>>>>>>>
>>>>>>> BiasCorrectionType: 0
>>>>>>> UseLLS_Recompute_Means: 0
>>>>>>> BiasCorrectionType: 0
>>>>>>> UseLLS_Recompute_Means: 0
>>>>>>> BiasCorrectionType: 0
>>>>>>> UseLLS_Recompute_Means: 0
>>>>>>> [EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 1. Define Task
>>>>>>> onEntryInternal - entering input from 2. Define Input Datasets
>>>>>>> processingAfterOnEntry
>>>>>>> updateClientArea - hiding 1. Define Task
>>>>>>> showUserInterface - showing 2. Define Input Datasets
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>> Sourcing general Task file :
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>>
>>>>>>> Sourcing task specific file:
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>>
>>>>>>> goToStep - Attempting to go to finish step Segment
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 2. Define Input Datasets
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 2. Define Input Datasets
>>>>>>> onEntryInternal - entering input from 3. Define Anatomical Tree
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 3. Define Anatomical Tree
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 3. Define Anatomical Tree
>>>>>>> onEntryInternal - entering input from 4. Define Atlas
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 4. Define Atlas
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 4. Define Atlas
>>>>>>> onEntryInternal - entering input from 5. Edit Registration Parameters
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 5. Edit Registration
>>>>>>> Parameters
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 5. Edit Registration Parameters
>>>>>>> onEntryInternal - entering input from 6. Define Preprocessing
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>>
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> Sourcing general Task file :
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>>
>>>>>>> Sourcing task specific file:
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>> Sourcing general Task file :
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>>
>>>>>>> Sourcing task specific file:
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>> couldn't read file
>>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>>> no such file or directory
>>>>>>> couldn't read file
>>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>>> no such file or directory
>>>>>>>         while executing
>>>>>>> "source
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
>>>>>>> TCL: ==========================================
>>>>>>> TCL: == Init Variables
>>>>>>> TCL: ==========================================
>>>>>>> TCL: User selected BRAINS
>>>>>>> TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
>>>>>>>
>>>>>>>
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 6. Define Preprocessing
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 6. Define Preprocessing
>>>>>>>
>>>>>>> Traceback (most recent call last):
>>>>>>>       File
>>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>>> line 121, in onExit
>>>>>>>         self.runPreProcessing()
>>>>>>>       File
>>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>>> line 130, in runPreProcessing
>>>>>>>         message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please
>>>>>>> wait", "Please wait while pre-processing runs..",
>>>>>>> qt.QMessageBox.Ignore )
>>>>>>> ValueError: Could not find matching overload for given arguments:
>>>>>>> (0, 'Please wait', 'Please wait while pre-processing 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)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>> Sent: Sunday, April 15, 2012 7:02 PM
>>>>>>> To: He,Renjie
>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>
>>>>>>> Renje: One window could you do the following for me :
>>>>>>>
>>>>>>> after you get to the segment step where nothing is happening could
>>>>>>> you
>>>>>>> go to the top menu ->      View ->      Error Log ->      select each
>>>>>>> entry and copy
>>>>>>> /past the text in the frame below in this email. I know this is a
>>>>>>> little
>>>>>>> bit cumbersome but do not know how else to help you otherwise
>>>>>>>
>>>>>>> Steve: is there an easy way to get the log under Windows ?
>>>>>>>
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Kilian
>>>>>>>
>>>>>>> On 04/13/2012 05:07 PM, He,Renjie wrote:
>>>>>>>> Thanks! At least the Mac OS is working!
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>> Sent: Friday, April 13, 2012 4:03 PM
>>>>>>>> To: He,Renjie
>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>
>>>>>>>> no - I will let you know in a little bit how to send me the log
>>>>>>>> files
>>>>>>>>
>>>>>>>> K
>>>>>>>> On 4/13/2012 4:57 PM, He,Renjie wrote:
>>>>>>>>> All our Win systems are 32-bits, could this be the point?
>>>>>>>>>
>>>>>>>>> ________________________________________
>>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>>> Sent: Friday, April 13, 2012 3:34 PM
>>>>>>>>> To: He,Renjie
>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> I know that others are using the software and do not run into these
>>>>>>>>> problems. So if it happens to you then we have to dig a little bit
>>>>>>>>> deeper :)
>>>>>>>>>
>>>>>>>>> Kilian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/13/2012 4:23 PM, He,Renjie wrote:
>>>>>>>>>> Hi, Kilian,
>>>>>>>>>>
>>>>>>>>>> We did exactly what you mentioned! I will try it again on Mac
>>>>>>>>>> OS and get back to you afterwards. Thanks!
>>>>>>>>>>
>>>>>>>>>> ________________________________________
>>>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>>>> Sent: Friday, April 13, 2012 3:16 PM
>>>>>>>>>> To: He,Renjie
>>>>>>>>>> Cc: Pohl, Kilian; Sonia Pujol
>>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> Slicer 3.6.3 is not supported . What tutorial did you use ?
>>>>>>>>>>
>>>>>>>>>> Could you do a simple test?
>>>>>>>>>>
>>>>>>>>>>          Load in an MR image, select the task MRI Human Brain in
>>>>>>>>>> the
>>>>>>>>>> EMSegmenter and press the simple mode button. Then simply
>>>>>>>>>> select the MR
>>>>>>>>>> scan you just loaded in and press segment. This should
>>>>>>>>>> definitely work
>>>>>>>>>> on MAC with the 4.10. version. The other versions should be
>>>>>>>>>> ignored.
>>>>>>>>>>
>>>>>>>>>> Once it works on a mac could you try it out on your windows
>>>>>>>>>> machines  ?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Kilian
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 4/13/2012 4:07 PM, He,Renjie wrote:
>>>>>>>>>>> Hi, Kilian,
>>>>>>>>>>>
>>>>>>>>>>> Thanks for the email! Our systems are:
>>>>>>>>>>>
>>>>>>>>>>> Desktop: Mac OS x 10.6 64-bit
>>>>>>>>>>>                         Win XP Pro 32-bit
>>>>>>>>>>>
>>>>>>>>>>> Laptop: Win Vista Home 32-bit
>>>>>>>>>>>
>>>>>>>>>>> we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the
>>>>>>>>>>> simple mode of EMsegment with altas according to the steps in
>>>>>>>>>>> the tutorial and the results are:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 3.6.3: all gave the errors of scalar type mismatch
>>>>>>>>>>> 4.0.1: all failed to reponse the buttom of segment
>>>>>>>>>>> 4.1.0: all give the message "segmentation did not execute
>>>>>>>>>>> correctly!".
>>>>>>>>>>>
>>>>>>>>>>> Where could I find the log files?
>>>>>>>>>>>
>>>>>>>>>>> Thank again!
>>>>>>>>>>>
>>>>>>>>>>> Renjie
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ________________________________________
>>>>>>>>>>> From: Pohl, Kilian [[hidden email]]
>>>>>>>>>>> Sent: Friday, April 13, 2012 2:52 PM
>>>>>>>>>>> To: He,Renjie; Sonia Pujol; [hidden email]
>>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>>
>>>>>>>>>>> Hi Renjie,
>>>>>>>>>>>
>>>>>>>>>>> What version of Slicer are you running, can you provide us
>>>>>>>>>>> with the log file, what operating system are you using (e.g.
>>>>>>>>>>> XP 64 bit) and what task are you executing ?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Kilian
>>>>>>>>>>>
>>>>>>>>>>> Ps: Please send me responds back to [hidden email]
>>>>>>>>>>>
>>>>>>>>>>> -----Original Message-----
>>>>>>>>>>> From: He,Renjie [mailto:[hidden email]]
>>>>>>>>>>> Sent: Fri 4/13/2012 2:04 PM
>>>>>>>>>>> To: Sonia Pujol
>>>>>>>>>>> Cc: Pohl, Kilian
>>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>>
>>>>>>>>>>> yes, it got the same message as "segmentation did not execute
>>>>>>>>>>> correctly!".
>>>>>>>>>>>
>>>>>>>>>>> ________________________________
>>>>>>>>>>> From: Sonia Pujol [[hidden email]]
>>>>>>>>>>> Sent: Friday, April 13, 2012 12:35 PM
>>>>>>>>>>> To: He,Renjie
>>>>>>>>>>> Cc: [hidden email]
>>>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>>>
>>>>>>>>>>> Hi Renjie,
>>>>>>>>>>>
>>>>>>>>>>> Which version of Slicer are you using ? I have cc-ed Kilian
>>>>>>>>>>> Polh who may have useful insights since he developed the
>>>>>>>>>>> EMSegmenter.
>>>>>>>>>>>
>>>>>>>>>>> Best Regards,
>>>>>>>>>>>
>>>>>>>>>>> Sonia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 4/13/12 12:49 PM, He,Renjie wrote:
>>>>>>>>>>> Dear Dr. Pujol,
>>>>>>>>>>>
>>>>>>>>>>> Sorry to bother you! We tried to make the EMsegmenter work but
>>>>>>>>>>> totally failed. On desktops (with Mac OS and Win XP), when
>>>>>>>>>>> click on the segment button, there is no response. On one
>>>>>>>>>>> laptop with Win Vista, the segmentation failed and get
>>>>>>>>>>> "segmentation did not execute correctly!". Could you please
>>>>>>>>>>> give us some hints, Many thanks!
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>> Renjie He
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Sonia Pujol, Ph.D.
>>>>>>>>>>> Surgical Planning Laboratory, Harvard Medical School
>>>>>>>>>>> Brigham and Women's Hospital, Boston, MA
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The information contained in this e-mail message is intended
>>>>>>>>>>> only for the personal and confidential use of the recipient(s)
>>>>>>>>>>> named above. If the reader of this message is not the intended
>>>>>>>>>>> recipient or an agent responsible for delivering it to the
>>>>>>>>>>> intended recipient, you are hereby notified that you have
>>>>>>>>>>> received this document in error and that any review,
>>>>>>>>>>> dissemination, distribution, or copying of this message is
>>>>>>>>>>> strictly prohibited. If you have received this communication
>>>>>>>>>>> in error, please notify us immediately by e-mail, and delete
>>>>>>>>>>> the original message.
>>>
>>> _______________________________________________
>>> 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: EMsegmenter would not work

Julien Finet
Kilian,

I just added some documentation for the Modules settings:

You'll get more information about the color coding used in the Modules list. 

Please let me know if it's not clear. 

Thanks,
Julien.

On Thu, Apr 26, 2012 at 11:56 AM, Kilian Pohl <[hidden email]> wrote:
is there an easy way for Renjie to find out which dependencies failed ?

Kilian
On 4/26/2012 11:00 AM, Andriy Fedorov wrote:
> On Thu, Apr 26, 2012 at 10:54 AM, Nicole Aucoin<[hidden email]>  wrote:
>> The module failed to load. When I start up slicer without CLI modules I
>> get this message in the terminal:
>> Loading module "CropVolume"
>> RegisterIO "qSlicerVolumesIO"
>> When loading module  "CropVolume" , the dependency
>> "ResampleScalarVectorDWIVolume" failed to be loaded.
>>
> I wonder if it makes sense to add a popup warning window to notify the
> users when a dependency fails for a selected module.
>
> In my opinion, it would make more sense not to load modules with
> failed dependencies at all.
>
>> and in Edit ->  Application Settings ->  Module Settings, CropVolume is in
>> red.
>>
>> Nicole
>>
>> On 04/26/2012 10:38 AM, Kilian Pohl wrote:
>>> Does anybody know what it means if a module is in red color ?
>>>
>>> K
>>>
>>> -------- Original Message --------
>>> Subject:      RE: EMsegmenter would not work
>>> Date:         Thu, 26 Apr 2012 09:26:12 -0500
>>> From:         He,Renjie<[hidden email]>
>>> To:   Kilian Pohl<[hidden email]>
>>>
>>>
>>>
>>> one more observation:
>>>
>>> when I click Edit->Modules settings, I found "EMSegmenter with altas" is in red color, while all others are in black.
>>>
>>> Renjie
>>>
>>>
>>> On 4/26/2012 10:36 AM, Kilian Pohl wrote:
>>>> Hi Renjie,
>>>>
>>>> On 4/26/2012 10:24 AM, He,Renjie wrote:
>>>>> Dear Kilian,
>>>>>
>>>>> I did all you mentioned, after run the simple segmentation on
>>>>> version 4.1.0, after a flash of altas on screen, it gives the same
>>>>> message: "segmentation did not execute correctly!".
>>>>>
>>>>> The files generated during segmentation procedures are: pos files,
>>>>> aligned altas files, aligned t1 file, but deformVolume and EM_map
>>>>> are empty.
>>>> Are you running simple or advanced mode ? If you ran it in simple
>>>> mode could you switch to advance mode and let me know exactly after
>>>> which step you get an error message ?
>>>>
>>>> Did you delete the directory ? Could you just send me the log that
>>>> lists all the tasks that are added to the list similar to
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>>> File :
>>>>
>>>> ...
>>>> in my previous email
>>>>
>>>> Thanks
>>>>
>>>> Kilian
>>>>
>>>>
>>>>
>>>>
>>>>> Renjie
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: Kilian Pohl [[hidden email]]
>>>>> Sent: Wednesday, April 25, 2012 6:56 PM
>>>>> To: He,Renjie
>>>>> Subject: Re: EMsegmenter would not work
>>>>>
>>>>> Hi Renjie,
>>>>>
>>>>> I assume you run into this problem when you run Slicer 4.1.0 and not
>>>>> 4.0.1- correct ? I just installed it on my machine and it runs fine .
>>>>> One thing I noticed is that you have in
>>>>>
>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\
>>>>>
>>>>> a couple of tasks that are not valid anymore . Could you do me a
>>>>> favour and remove the file
>>>>>
>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy
>>>>>
>>>>> and restart Slicer as well as run the EMSegmenter ?
>>>>>
>>>>> The directory should list the following mrml files :
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>>>> File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>>> Full Parcellation'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>>> Hemisphere'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>>> Parcellation'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
>>>>> Brain'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>
>>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
>>>>> Primate'  File :
>>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>>
>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>        from: D:/pieper/Slicer4.1/Slicer
>>>>> 4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
>>>>>        to:
>>>>> C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy
>>>>>
>>>>> Also do you mind if I post the next message on the slicer devel list so
>>>>> that other can follow the track too ? Ron asked me to do that
>>>>>
>>>>> Kilian
>>>>>
>>>>>
>>>>> On 04/16/2012 06:06 PM, He,Renjie wrote:
>>>>>> Thanks for your attention!
>>>>>>
>>>>>> ________________________________________
>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>> Sent: Monday, April 16, 2012 4:57 PM
>>>>>> To: He,Renjie
>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>
>>>>>> This helps a lot - I will further investigate next week
>>>>>>
>>>>>> Kilian
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 4/16/2012 10:06 AM, He,Renjie wrote:
>>>>>>> Dear Kilian,
>>>>>>>
>>>>>>> Thank you so much for your time and help!
>>>>>>>
>>>>>>> Here is the message for version 4.1.0 : "segmentation did not
>>>>>>> execute correctly!".
>>>>>>> and log error:
>>>>>>> ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line
>>>>>>> 2162
>>>>>>> vtkEMSegmentLogic (1E2E6F10): Exception thrown during
>>>>>>> segmentation: bad allocation
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Here is the log for version 4.0.1 :
>>>>>>>
>>>>>>> Show module (name): "EMSegment"
>>>>>>> onEntryInternal - entering input from 1. Define Task
>>>>>>> processingAfterOnEntry
>>>>>>> showUserInterface - showing 1. Define Task
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand
>>>>>>> Bone'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human
>>>>>>> Eye'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
>>>>>>>
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion
>>>>>>> Exp'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Exp'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Full Parcellation'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Hemisphere'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain HIPR'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain Parcellation'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>>> Brain'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human
>>>>>>> Primate'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas
>>>>>>> Cluster'  File :
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 1. Define Task
>>>>>>>
>>>>>>> [EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI
>>>>>>> Human Brain' from file
>>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>>>
>>>>>>> ==========================================================================
>>>>>>>
>>>>>>> == Completed importing data
>>>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
>>>>>>> ==========================================================================
>>>>>>>
>>>>>>> BiasCorrectionType: 0
>>>>>>> UseLLS_Recompute_Means: 0
>>>>>>> BiasCorrectionType: 0
>>>>>>> UseLLS_Recompute_Means: 0
>>>>>>> BiasCorrectionType: 0
>>>>>>> UseLLS_Recompute_Means: 0
>>>>>>> [EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 1. Define Task
>>>>>>> onEntryInternal - entering input from 2. Define Input Datasets
>>>>>>> processingAfterOnEntry
>>>>>>> updateClientArea - hiding 1. Define Task
>>>>>>> showUserInterface - showing 2. Define Input Datasets
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>> Sourcing general Task file :
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>>
>>>>>>> Sourcing task specific file:
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>>
>>>>>>> goToStep - Attempting to go to finish step Segment
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 2. Define Input Datasets
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 2. Define Input Datasets
>>>>>>> onEntryInternal - entering input from 3. Define Anatomical Tree
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 3. Define Anatomical Tree
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 3. Define Anatomical Tree
>>>>>>> onEntryInternal - entering input from 4. Define Atlas
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 4. Define Atlas
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 4. Define Atlas
>>>>>>> onEntryInternal - entering input from 5. Edit Registration Parameters
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 5. Edit Registration
>>>>>>> Parameters
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 5. Edit Registration Parameters
>>>>>>> onEntryInternal - entering input from 6. Define Preprocessing
>>>>>>> processingAfterOnEntry
>>>>>>> goForward - posting ValidationTransition
>>>>>>>
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> Sourcing general Task file :
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>>
>>>>>>> Sourcing task specific file:
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>>
>>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>>      from:
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>>      to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>> Sourcing general Task file :
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>>
>>>>>>> Sourcing task specific file:
>>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>> couldn't read file
>>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>>> no such file or directory
>>>>>>> couldn't read file
>>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>>> no such file or directory
>>>>>>>         while executing
>>>>>>> "source
>>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
>>>>>>> TCL: ==========================================
>>>>>>> TCL: == Init Variables
>>>>>>> TCL: ==========================================
>>>>>>> TCL: User selected BRAINS
>>>>>>> TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
>>>>>>>
>>>>>>>
>>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>>> validateInternal - validating input from 6. Define Preprocessing
>>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>>> onExitInternal - exiting 6. Define Preprocessing
>>>>>>>
>>>>>>> Traceback (most recent call last):
>>>>>>>       File
>>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>>> line 121, in onExit
>>>>>>>         self.runPreProcessing()
>>>>>>>       File
>>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>>> line 130, in runPreProcessing
>>>>>>>         message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please
>>>>>>> wait", "Please wait while pre-processing runs..",
>>>>>>> qt.QMessageBox.Ignore )
>>>>>>> ValueError: Could not find matching overload for given arguments:
>>>>>>> (0, 'Please wait', 'Please wait while pre-processing 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)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>> Sent: Sunday, April 15, 2012 7:02 PM
>>>>>>> To: He,Renjie
>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>
>>>>>>> Renje: One window could you do the following for me :
>>>>>>>
>>>>>>> after you get to the segment step where nothing is happening could
>>>>>>> you
>>>>>>> go to the top menu ->      View ->      Error Log ->      select each
>>>>>>> entry and copy
>>>>>>> /past the text in the frame below in this email. I know this is a
>>>>>>> little
>>>>>>> bit cumbersome but do not know how else to help you otherwise
>>>>>>>
>>>>>>> Steve: is there an easy way to get the log under Windows ?
>>>>>>>
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Kilian
>>>>>>>
>>>>>>> On 04/13/2012 05:07 PM, He,Renjie wrote:
>>>>>>>> Thanks! At least the Mac OS is working!
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>> Sent: Friday, April 13, 2012 4:03 PM
>>>>>>>> To: He,Renjie
>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>
>>>>>>>> no - I will let you know in a little bit how to send me the log
>>>>>>>> files
>>>>>>>>
>>>>>>>> K
>>>>>>>> On 4/13/2012 4:57 PM, He,Renjie wrote:
>>>>>>>>> All our Win systems are 32-bits, could this be the point?
>>>>>>>>>
>>>>>>>>> ________________________________________
>>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>>> Sent: Friday, April 13, 2012 3:34 PM
>>>>>>>>> To: He,Renjie
>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> I know that others are using the software and do not run into these
>>>>>>>>> problems. So if it happens to you then we have to dig a little bit
>>>>>>>>> deeper :)
>>>>>>>>>
>>>>>>>>> Kilian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/13/2012 4:23 PM, He,Renjie wrote:
>>>>>>>>>> Hi, Kilian,
>>>>>>>>>>
>>>>>>>>>> We did exactly what you mentioned! I will try it again on Mac
>>>>>>>>>> OS and get back to you afterwards. Thanks!
>>>>>>>>>>
>>>>>>>>>> ________________________________________
>>>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>>>> Sent: Friday, April 13, 2012 3:16 PM
>>>>>>>>>> To: He,Renjie
>>>>>>>>>> Cc: Pohl, Kilian; Sonia Pujol
>>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> Slicer 3.6.3 is not supported . What tutorial did you use ?
>>>>>>>>>>
>>>>>>>>>> Could you do a simple test?
>>>>>>>>>>
>>>>>>>>>>          Load in an MR image, select the task MRI Human Brain in
>>>>>>>>>> the
>>>>>>>>>> EMSegmenter and press the simple mode button. Then simply
>>>>>>>>>> select the MR
>>>>>>>>>> scan you just loaded in and press segment. This should
>>>>>>>>>> definitely work
>>>>>>>>>> on MAC with the 4.10. version. The other versions should be
>>>>>>>>>> ignored.
>>>>>>>>>>
>>>>>>>>>> Once it works on a mac could you try it out on your windows
>>>>>>>>>> machines  ?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Kilian
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 4/13/2012 4:07 PM, He,Renjie wrote:
>>>>>>>>>>> Hi, Kilian,
>>>>>>>>>>>
>>>>>>>>>>> Thanks for the email! Our systems are:
>>>>>>>>>>>
>>>>>>>>>>> Desktop: Mac OS x 10.6 64-bit
>>>>>>>>>>>                         Win XP Pro 32-bit
>>>>>>>>>>>
>>>>>>>>>>> Laptop: Win Vista Home 32-bit
>>>>>>>>>>>
>>>>>>>>>>> we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the
>>>>>>>>>>> simple mode of EMsegment with altas according to the steps in
>>>>>>>>>>> the tutorial and the results are:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 3.6.3: all gave the errors of scalar type mismatch
>>>>>>>>>>> 4.0.1: all failed to reponse the buttom of segment
>>>>>>>>>>> 4.1.0: all give the message "segmentation did not execute
>>>>>>>>>>> correctly!".
>>>>>>>>>>>
>>>>>>>>>>> Where could I find the log files?
>>>>>>>>>>>
>>>>>>>>>>> Thank again!
>>>>>>>>>>>
>>>>>>>>>>> Renjie
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ________________________________________
>>>>>>>>>>> From: Pohl, Kilian [[hidden email]]
>>>>>>>>>>> Sent: Friday, April 13, 2012 2:52 PM
>>>>>>>>>>> To: He,Renjie; Sonia Pujol; [hidden email]
>>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>>
>>>>>>>>>>> Hi Renjie,
>>>>>>>>>>>
>>>>>>>>>>> What version of Slicer are you running, can you provide us
>>>>>>>>>>> with the log file, what operating system are you using (e.g.
>>>>>>>>>>> XP 64 bit) and what task are you executing ?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Kilian
>>>>>>>>>>>
>>>>>>>>>>> Ps: Please send me responds back to [hidden email]
>>>>>>>>>>>
>>>>>>>>>>> -----Original Message-----
>>>>>>>>>>> From: He,Renjie [mailto:[hidden email]]
>>>>>>>>>>> Sent: Fri 4/13/2012 2:04 PM
>>>>>>>>>>> To: Sonia Pujol
>>>>>>>>>>> Cc: Pohl, Kilian
>>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>>
>>>>>>>>>>> yes, it got the same message as "segmentation did not execute
>>>>>>>>>>> correctly!".
>>>>>>>>>>>
>>>>>>>>>>> ________________________________
>>>>>>>>>>> From: Sonia Pujol [[hidden email]]
>>>>>>>>>>> Sent: Friday, April 13, 2012 12:35 PM
>>>>>>>>>>> To: He,Renjie
>>>>>>>>>>> Cc: [hidden email]
>>>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>>>
>>>>>>>>>>> Hi Renjie,
>>>>>>>>>>>
>>>>>>>>>>> Which version of Slicer are you using ? I have cc-ed Kilian
>>>>>>>>>>> Polh who may have useful insights since he developed the
>>>>>>>>>>> EMSegmenter.
>>>>>>>>>>>
>>>>>>>>>>> Best Regards,
>>>>>>>>>>>
>>>>>>>>>>> Sonia
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 4/13/12 12:49 PM, He,Renjie wrote:
>>>>>>>>>>> Dear Dr. Pujol,
>>>>>>>>>>>
>>>>>>>>>>> Sorry to bother you! We tried to make the EMsegmenter work but
>>>>>>>>>>> totally failed. On desktops (with Mac OS and Win XP), when
>>>>>>>>>>> click on the segment button, there is no response. On one
>>>>>>>>>>> laptop with Win Vista, the segmentation failed and get
>>>>>>>>>>> "segmentation did not execute correctly!". Could you please
>>>>>>>>>>> give us some hints, Many thanks!
>>>>>>>>>>>
>>>>>>>>>>> Best regards,
>>>>>>>>>>> Renjie He
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Sonia Pujol, Ph.D.
>>>>>>>>>>> Surgical Planning Laboratory, Harvard Medical School
>>>>>>>>>>> Brigham and Women's Hospital, Boston, MA
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The information contained in this e-mail message is intended
>>>>>>>>>>> only for the personal and confidential use of the recipient(s)
>>>>>>>>>>> named above. If the reader of this message is not the intended
>>>>>>>>>>> recipient or an agent responsible for delivering it to the
>>>>>>>>>>> intended recipient, you are hereby notified that you have
>>>>>>>>>>> received this document in error and that any review,
>>>>>>>>>>> dissemination, distribution, or copying of this message is
>>>>>>>>>>> strictly prohibited. If you have received this communication
>>>>>>>>>>> in error, please notify us immediately by e-mail, and delete
>>>>>>>>>>> the original message.
>>>
>>> _______________________________________________
>>> slicer-users mailing list
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>>> 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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Customization for point size etc

Murat Maga

Hi,

 

Is there a way to customize the default size or the symbol for fiducials in 4.1? It is a bit tedious to go one by one.

 

M

 


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Re: Customization for point size etc

Aucoin, Nicole
Hello,

Not yet, that's planned for 4.2.

Nicole

On 04/26/2012 02:41 PM, Murat Maga wrote:

>
> Hi,
>
> Is there a way to customize the default size or the symbol for
> fiducials in 4.1? It is a bit tedious to go one by one.
>
> M
>
>
> _______________________________________________
> 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: EMsegmenter would not work

Julien Finet
In reply to this post by Andrey Fedorov
I wonder if it makes sense to add a popup warning window to notify the
users when a dependency fails for a selected module.
A module that fails to load should only be happening at developing stage. 
Therefore I wouldn't bother adding a message box but instead inform developers to check the logs. The error explaining why the module fails to load should be printed in the logs. 

In my opinion, it would make more sense not to load modules with
failed dependencies at all.
Already the case.

Julien. 

> and in Edit -> Application Settings -> Module Settings, CropVolume is in
> red.
>
> Nicole
>
> On 04/26/2012 10:38 AM, Kilian Pohl wrote:
>> Does anybody know what it means if a module is in red color ?
>>
>> K
>>
>> -------- Original Message --------
>> Subject:      RE: EMsegmenter would not work
>> Date:         Thu, 26 Apr 2012 09:26:12 -0500
>> From:         He,Renjie <[hidden email]>
>> To:   Kilian Pohl <[hidden email]>
>>
>>
>>
>> one more observation:
>>
>> when I click Edit->Modules settings, I found "EMSegmenter with altas" is in red color, while all others are in black.
>>
>> Renjie
>>
>>
>> On 4/26/2012 10:36 AM, Kilian Pohl wrote:
>>> Hi Renjie,
>>>
>>> On 4/26/2012 10:24 AM, He,Renjie wrote:
>>>> Dear Kilian,
>>>>
>>>> I did all you mentioned, after run the simple segmentation on
>>>> version 4.1.0, after a flash of altas on screen, it gives the same
>>>> message: "segmentation did not execute correctly!".
>>>>
>>>> The files generated during segmentation procedures are: pos files,
>>>> aligned altas files, aligned t1 file, but deformVolume and EM_map
>>>> are empty.
>>> Are you running simple or advanced mode ? If you ran it in simple
>>> mode could you switch to advance mode and let me know exactly after
>>> which step you get an error message ?
>>>
>>> Did you delete the directory ? Could you just send me the log that
>>> lists all the tasks that are added to the list similar to
>>>
>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>> File :
>>>
>>> ...
>>> in my previous email
>>>
>>> Thanks
>>>
>>> Kilian
>>>
>>>
>>>
>>>
>>>>
>>>> Renjie
>>>>
>>>>
>>>> ________________________________________
>>>> From: Kilian Pohl [[hidden email]]
>>>> Sent: Wednesday, April 25, 2012 6:56 PM
>>>> To: He,Renjie
>>>> Subject: Re: EMsegmenter would not work
>>>>
>>>> Hi Renjie,
>>>>
>>>> I assume you run into this problem when you run Slicer 4.1.0 and not
>>>> 4.0.1- correct ? I just installed it on my machine and it runs fine .
>>>> One thing I noticed is that you have in
>>>>
>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\
>>>>
>>>> a couple of tasks that are not valid anymore . Could you do me a
>>>> favour and remove the file
>>>>
>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy
>>>>
>>>> and restart Slicer as well as run the EMSegmenter ?
>>>>
>>>> The directory should list the following mrml files :
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'CT Hand Bone'
>>>> File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>> Full Parcellation'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>> Hemisphere'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human Brain
>>>> Parcellation'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'MRI Human
>>>> Brain'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>
>>>> [EMSegmentPy 04/26/2012 00:45:59]: Added to List Task: 'Non Human
>>>> Primate'  File :
>>>> 'C:\Users\ADMINI~1\AppData\Local\Temp\2\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>
>>>> GetTclTaskDirectory::Copying task files ...
>>>>       from: D:/pieper/Slicer4.1/Slicer
>>>> 4.1.0/share/Slicer-4.1/qt-loadable-modules/EMSegment/Tasks
>>>>       to:
>>>> C:/Users/ADMINI~1/AppData/Local/Temp/2/Slicer/EMSegmentTaskCopy
>>>>
>>>> Also do you mind if I post the next message on the slicer devel list so
>>>> that other can follow the track too ? Ron asked me to do that
>>>>
>>>> Kilian
>>>>
>>>>
>>>> On 04/16/2012 06:06 PM, He,Renjie wrote:
>>>>> Thanks for your attention!
>>>>>
>>>>> ________________________________________
>>>>> From: Kilian Pohl [[hidden email]]
>>>>> Sent: Monday, April 16, 2012 4:57 PM
>>>>> To: He,Renjie
>>>>> Subject: Re: EMsegmenter would not work
>>>>>
>>>>> This helps a lot - I will further investigate next week
>>>>>
>>>>> Kilian
>>>>>
>>>>>
>>>>>
>>>>> On 4/16/2012 10:06 AM, He,Renjie wrote:
>>>>>> Dear Kilian,
>>>>>>
>>>>>> Thank you so much for your time and help!
>>>>>>
>>>>>> Here is the message for version 4.1.0 : "segmentation did not
>>>>>> execute correctly!".
>>>>>> and log error:
>>>>>> ERROR: In ..\..\..\..\..\..\EMSegment\vtkEMSegmentLogic.cxx, line
>>>>>> 2162
>>>>>> vtkEMSegmentLogic (1E2E6F10): Exception thrown during
>>>>>> segmentation: bad allocation
>>>>>>
>>>>>>
>>>>>>
>>>>>> Here is the log for version 4.0.1 :
>>>>>>
>>>>>> Show module (name): "EMSegment"
>>>>>> onEntryInternal - entering input from 1. Define Task
>>>>>> processingAfterOnEntry
>>>>>> showUserInterface - showing 1. Define Task
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'CT Hand
>>>>>> Bone'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\CT-Hand-Bone.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Human
>>>>>> Eye'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Human-Eye.mrml'
>>>>>>
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Lesion
>>>>>> Exp'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Lesion-Exp.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Exp'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Exp.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Full Parcellation'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Full-Parcellation.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Hemisphere'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Hemisphere.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain HIPR'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-HIPR.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain Parcellation'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain-Parcellation.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'MRI Human
>>>>>> Brain'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Non Human
>>>>>> Primate'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Non-Human-Primate.mrml'
>>>>>> [EMSegmentPy 04/16/2012 08:59:15]: Added to List Task: 'Test Atlas
>>>>>> Cluster'  File :
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\Test-Atlas-Cluster.mrml'
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 1. Define Task
>>>>>>
>>>>>> [EMSegmentPy 04/16/2012 08:59:17]: Attempting to load task 'MRI
>>>>>> Human Brain' from file
>>>>>> 'C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml'
>>>>>>
>>>>>> ==========================================================================
>>>>>>
>>>>>> == Completed importing data
>>>>>> C:\DOCUME~1\rhe1\LOCALS~1\Temp\Slicer\EMSegmentTaskCopy\MRI-Human-Brain.mrml
>>>>>> ==========================================================================
>>>>>>
>>>>>> BiasCorrectionType: 0
>>>>>> UseLLS_Recompute_Means: 0
>>>>>> BiasCorrectionType: 0
>>>>>> UseLLS_Recompute_Means: 0
>>>>>> BiasCorrectionType: 0
>>>>>> UseLLS_Recompute_Means: 0
>>>>>> [EMSegmentPy 04/16/2012 08:59:18]: Loading completed.
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 1. Define Task
>>>>>> onEntryInternal - entering input from 2. Define Input Datasets
>>>>>> processingAfterOnEntry
>>>>>> updateClientArea - hiding 1. Define Task
>>>>>> showUserInterface - showing 2. Define Input Datasets
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>> Sourcing general Task file :
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>
>>>>>> Sourcing task specific file:
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>>
>>>>>> goToStep - Attempting to go to finish step Segment
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 2. Define Input Datasets
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 2. Define Input Datasets
>>>>>> onEntryInternal - entering input from 3. Define Anatomical Tree
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 3. Define Anatomical Tree
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 3. Define Anatomical Tree
>>>>>> onEntryInternal - entering input from 4. Define Atlas
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 4. Define Atlas
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 4. Define Atlas
>>>>>> onEntryInternal - entering input from 5. Edit Registration Parameters
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 5. Edit Registration
>>>>>> Parameters
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 5. Edit Registration Parameters
>>>>>> onEntryInternal - entering input from 6. Define Preprocessing
>>>>>> processingAfterOnEntry
>>>>>> goForward - posting ValidationTransition
>>>>>>
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> Sourcing general Task file :
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>
>>>>>> Sourcing task specific file:
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>>
>>>>>> GetTclTaskDirectory::Copying task files ...
>>>>>>     from:
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment/Tasks
>>>>>>     to: C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy
>>>>>> Sourcing general Task file :
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
>>>>>>
>>>>>> Sourcing task specific file:
>>>>>> C:/DOCUME~1/rhe1/LOCALS~1/Temp/Slicer/EMSegmentTaskCopy/MRI-Human-Brain.tcl
>>>>>> couldn't read file
>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>> no such file or directory
>>>>>> couldn't read file
>>>>>> "C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegmentTclEMSegmentAutoSample.tcl":
>>>>>> no such file or directory
>>>>>>        while executing
>>>>>> "source
>>>>>> C:/Slicer401/share/Slicer-4.0/qt-loadable-modules/EMSegment\Tcl\EMSegmentAutoSample.tcl"
>>>>>> TCL: ==========================================
>>>>>> TCL: == Init Variables
>>>>>> TCL: ==========================================
>>>>>> TCL: User selected BRAINS
>>>>>> TCLMRI: Preprocessing MRI Human Brain - ShowUserInterface
>>>>>>
>>>>>>
>>>>>> attemptToGoToNextStep - Attempting to go to the next step
>>>>>> validateInternal - validating input from 6. Define Preprocessing
>>>>>> goToNextStepAfterSuccessfulValidation - Calidation succeeded
>>>>>> goToNextStepAfterSuccessfulValidation - Posting TransitionToNextStep
>>>>>> performTransitionBetweenSteps - Performing transition between steps
>>>>>> onExitInternal - exiting 6. Define Preprocessing
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>>      File
>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>> line 121, in onExit
>>>>>>        self.runPreProcessing()
>>>>>>      File
>>>>>> "C:/Slicer401/lib/Slicer-4.0/qt-loadable-modules/Python\EMSegmentWizard\EMSegmentDefinePreprocessingStep.py",
>>>>>> line 130, in runPreProcessing
>>>>>>        message = qt.QMessageBox( qt.QMessageBox.NoIcon, "Please
>>>>>> wait", "Please wait while pre-processing runs..",
>>>>>> qt.QMessageBox.Ignore )
>>>>>> ValueError: Could not find matching overload for given arguments:
>>>>>> (0, 'Please wait', 'Please wait while pre-processing 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)
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ________________________________________
>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>> Sent: Sunday, April 15, 2012 7:02 PM
>>>>>> To: He,Renjie
>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>
>>>>>> Renje: One window could you do the following for me :
>>>>>>
>>>>>> after you get to the segment step where nothing is happening could
>>>>>> you
>>>>>> go to the top menu ->    View ->    Error Log ->    select each
>>>>>> entry and copy
>>>>>> /past the text in the frame below in this email. I know this is a
>>>>>> little
>>>>>> bit cumbersome but do not know how else to help you otherwise
>>>>>>
>>>>>> Steve: is there an easy way to get the log under Windows ?
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Kilian
>>>>>>
>>>>>> On 04/13/2012 05:07 PM, He,Renjie wrote:
>>>>>>> Thanks! At least the Mac OS is working!
>>>>>>>
>>>>>>> ________________________________________
>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>> Sent: Friday, April 13, 2012 4:03 PM
>>>>>>> To: He,Renjie
>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>
>>>>>>> no - I will let you know in a little bit how to send me the log
>>>>>>> files
>>>>>>>
>>>>>>> K
>>>>>>> On 4/13/2012 4:57 PM, He,Renjie wrote:
>>>>>>>> All our Win systems are 32-bits, could this be the point?
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>> Sent: Friday, April 13, 2012 3:34 PM
>>>>>>>> To: He,Renjie
>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>
>>>>>>>> I know that others are using the software and do not run into these
>>>>>>>> problems. So if it happens to you then we have to dig a little bit
>>>>>>>> deeper :)
>>>>>>>>
>>>>>>>> Kilian
>>>>>>>>
>>>>>>>>
>>>>>>>> On 4/13/2012 4:23 PM, He,Renjie wrote:
>>>>>>>>> Hi, Kilian,
>>>>>>>>>
>>>>>>>>> We did exactly what you mentioned! I will try it again on Mac
>>>>>>>>> OS and get back to you afterwards. Thanks!
>>>>>>>>>
>>>>>>>>> ________________________________________
>>>>>>>>> From: Kilian Pohl [[hidden email]]
>>>>>>>>> Sent: Friday, April 13, 2012 3:16 PM
>>>>>>>>> To: He,Renjie
>>>>>>>>> Cc: Pohl, Kilian; Sonia Pujol
>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>
>>>>>>>>> Slicer 3.6.3 is not supported . What tutorial did you use ?
>>>>>>>>>
>>>>>>>>> Could you do a simple test?
>>>>>>>>>
>>>>>>>>>         Load in an MR image, select the task MRI Human Brain in
>>>>>>>>> the
>>>>>>>>> EMSegmenter and press the simple mode button. Then simply
>>>>>>>>> select the MR
>>>>>>>>> scan you just loaded in and press segment. This should
>>>>>>>>> definitely work
>>>>>>>>> on MAC with the 4.10. version. The other versions should be
>>>>>>>>> ignored.
>>>>>>>>>
>>>>>>>>> Once it works on a mac could you try it out on your windows
>>>>>>>>> machines  ?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Kilian
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 4/13/2012 4:07 PM, He,Renjie wrote:
>>>>>>>>>> Hi, Kilian,
>>>>>>>>>>
>>>>>>>>>> Thanks for the email! Our systems are:
>>>>>>>>>>
>>>>>>>>>> Desktop: Mac OS x 10.6 64-bit
>>>>>>>>>>                        Win XP Pro 32-bit
>>>>>>>>>>
>>>>>>>>>> Laptop: Win Vista Home 32-bit
>>>>>>>>>>
>>>>>>>>>> we tried slicer version 3.6.3, 4.0.1 and 4.1.1 using the
>>>>>>>>>> simple mode of EMsegment with altas according to the steps in
>>>>>>>>>> the tutorial and the results are:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 3.6.3: all gave the errors of scalar type mismatch
>>>>>>>>>> 4.0.1: all failed to reponse the buttom of segment
>>>>>>>>>> 4.1.0: all give the message "segmentation did not execute
>>>>>>>>>> correctly!".
>>>>>>>>>>
>>>>>>>>>> Where could I find the log files?
>>>>>>>>>>
>>>>>>>>>> Thank again!
>>>>>>>>>>
>>>>>>>>>> Renjie
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ________________________________________
>>>>>>>>>> From: Pohl, Kilian [[hidden email]]
>>>>>>>>>> Sent: Friday, April 13, 2012 2:52 PM
>>>>>>>>>> To: He,Renjie; Sonia Pujol; [hidden email]
>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> Hi Renjie,
>>>>>>>>>>
>>>>>>>>>> What version of Slicer are you running, can you provide us
>>>>>>>>>> with the log file, what operating system are you using (e.g.
>>>>>>>>>> XP 64 bit) and what task are you executing ?
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Kilian
>>>>>>>>>>
>>>>>>>>>> Ps: Please send me responds back to [hidden email]
>>>>>>>>>>
>>>>>>>>>> -----Original Message-----
>>>>>>>>>> From: He,Renjie [mailto:[hidden email]]
>>>>>>>>>> Sent: Fri 4/13/2012 2:04 PM
>>>>>>>>>> To: Sonia Pujol
>>>>>>>>>> Cc: Pohl, Kilian
>>>>>>>>>> Subject: RE: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> yes, it got the same message as "segmentation did not execute
>>>>>>>>>> correctly!".
>>>>>>>>>>
>>>>>>>>>> ________________________________
>>>>>>>>>> From: Sonia Pujol [[hidden email]]
>>>>>>>>>> Sent: Friday, April 13, 2012 12:35 PM
>>>>>>>>>> To: He,Renjie
>>>>>>>>>> Cc: [hidden email]
>>>>>>>>>> Subject: Re: EMsegmenter would not work
>>>>>>>>>>
>>>>>>>>>> Hi Renjie,
>>>>>>>>>>
>>>>>>>>>> Which version of Slicer are you using ? I have cc-ed Kilian
>>>>>>>>>> Polh who may have useful insights since he developed the
>>>>>>>>>> EMSegmenter.
>>>>>>>>>>
>>>>>>>>>> Best Regards,
>>>>>>>>>>
>>>>>>>>>> Sonia
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 4/13/12 12:49 PM, He,Renjie wrote:
>>>>>>>>>> Dear Dr. Pujol,
>>>>>>>>>>
>>>>>>>>>> Sorry to bother you! We tried to make the EMsegmenter work but
>>>>>>>>>> totally failed. On desktops (with Mac OS and Win XP), when
>>>>>>>>>> click on the segment button, there is no response. On one
>>>>>>>>>> laptop with Win Vista, the segmentation failed and get
>>>>>>>>>> "segmentation did not execute correctly!". Could you please
>>>>>>>>>> give us some hints, Many thanks!
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>> Renjie He
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Sonia Pujol, Ph.D.
>>>>>>>>>> Surgical Planning Laboratory, Harvard Medical School
>>>>>>>>>> Brigham and Women's Hospital, Boston, MA
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The information contained in this e-mail message is intended
>>>>>>>>>> only for the personal and confidential use of the recipient(s)
>>>>>>>>>> named above. If the reader of this message is not the intended
>>>>>>>>>> recipient or an agent responsible for delivering it to the
>>>>>>>>>> intended recipient, you are hereby notified that you have
>>>>>>>>>> received this document in error and that any review,
>>>>>>>>>> dissemination, distribution, or copying of this message is
>>>>>>>>>> strictly prohibited. If you have received this communication
>>>>>>>>>> in error, please notify us immediately by e-mail, and delete
>>>>>>>>>> the original message.
>>>
>>
>>
>> _______________________________________________
>> slicer-users mailing list
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