Lupus Lesion Segmentation

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Lupus Lesion Segmentation

Arman Eshaghi
Dear Jeremy (Bockholt),

While I was running the tutorial data for Lupus White Matter Segmentation in slicer 3.6, the following errors stop the analyzing process of "Predict Lesions" procedure. 

ERROR: In /Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1497
vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions standard error:

PredictLesions(13725,0xa0814500) malloc: *** mmap(size=67108864) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
/Users/user/Slicer3user/13752/LesionSegmentationApplications/PredictLesions: exception caught !


And the final error:


ERROR: In /Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1522
vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions completed with errors


Thanks in advance,
Arman


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Re: Lupus Lesion Segmentation

Joel Laxamana
Hello,

I've also run into this problem.  Has there been any updates on how to solve this problem?  Also after the "Predict Lesions" run completes, the Status says "Completed with errors".

Here is my complete error log. It may help if you saw the whole log:


Begin error log
==================================================

Type: Error
Time: Wed May 25 17:05:04 2011
Description: ERROR: In /extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1524
vtkCommandLineModuleLogic (0xa3337b0): Predict Lesions completed with errors




Type: Error
Time: Wed May 25 17:05:04 2011
Description: ERROR: In /extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1499
vtkCommandLineModuleLogic (0xa3337b0): Predict Lesions standard error:

Can't read lesionSegmentation.model




Type: Information
Time: Wed May 25 17:05:04 2011
Description: Predict Lesions standard output:

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<filter-end>
<filter-time>1</filter-time>


Type: Information
Time: Wed May 25 16:51:31 2011
Description: Predict Lesions command line:

/home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/PredictLesions --inputT1Volume /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeJ.nrrd --inputT2Volume /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBA.nrrd --inputFLAIRVolume /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBB.nrrd --inputMaskVolume /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeF.nrrd --inputPercentThreshold 12 --inputModelFile lesionSegmentation.model --inputSVMModelFile svm.model --outputLesionMask /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBC.nrrd --outputLesionProb /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBD.nrrd


Type: Information
Time: Wed May 25 16:51:28 2011
Description: CommandLineModule

Type: Information
Time: Wed May 25 16:51:28 2011
Description: /home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/PredictLesions

Type: Information
Time: Wed May 25 16:51:28 2011
Description: Found CommandLine Module, target is

Type: Information
Time: Wed May 25 16:47:10 2011
Description: Joint Intensity Standardization completed without errors


Type: Information
Time: Wed May 25 16:47:10 2011
Description: Joint Intensity Standardization standard output:

<filter-end>
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<filter-time>3.19964</filter-time>
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<filter-time>2.43317</filter-time>
</filter-end><filter-end>
<filter-time>3.09205</filter-time>
</filter-end>

Type: Information
Time: Wed May 25 16:46:52 2011
Description: Joint Intensity Standardization command line:

/home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/IntensityStandardize --inputT1Mov /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeH.nrrd --inputT2Mov /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeI.nrrd --inputFLAIRMov /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeG.nrrd --inputMovMask /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeF.nrrd --inputT1Ref /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeD.nrrd --inputT2Ref /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeE.nrrd --inputFLAIRRef /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeC.nrrd --inputRefMask /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeB.nrrd --outputT1Mov /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeJ.nrrd --outputT2 /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBA.nrrd --outputFlair /home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBB.nrrd


Type: Information
Time: Wed May 25 16:46:45 2011
Description: CommandLineModule

Type: Information
Time: Wed May 25 16:46:45 2011
Description: /home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/IntensityStandardize

Type: Information
Time: Wed May 25 16:46:45 2011
Description: Found CommandLine Module, target is

Type: Warning
Time: Wed May 25 16:42:16 2011
Description: Warning: In /extra/pieper/slicer3/release/Slicer3/Libs/MRML/vtkMRMLCameraNode.cxx, line 449
vtkMRMLCameraNode (0xb89dbd0): SetActiveTag: vtkMRMLCameraNode1 found another node vtkMRMLCameraNode1 with the tag vtkMRMLViewNode1

=========================================================================
End error log

Any feedback to get any resolution to this will be appreciated.

Thanks in advance,
Joel
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Re: Lupus Lesion Segmentation

madanrao
In reply to this post by Arman Eshaghi
Hello,

It seems the error: malloc: *** mmap(size=67108864) failed (error code=12)
is due to failed memory allocation to a variable PredictLesions which can be due to a simple code error or
limited memory of the machine (which is more likely the cause).

Hope this helps.

AM Mohan Rao


 

On Fri, Jul 16, 2010 at 10:52 PM, Arman Eshaghi <[hidden email]> wrote:
Dear Jeremy (Bockholt),

While I was running the tutorial data for Lupus White Matter Segmentation in slicer 3.6, the following errors stop the analyzing process of "Predict Lesions" procedure. 

ERROR: In /Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1497
vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions standard error:

PredictLesions(13725,0xa0814500) malloc: *** mmap(size=67108864) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
/Users/user/Slicer3user/13752/LesionSegmentationApplications/PredictLesions: exception caught !


And the final error:


ERROR: In /Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1522
vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions completed with errors


Thanks in advance,
Arman


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Re: Lupus Lesion Segmentation

Scully, Mark S
In reply to this post by Arman Eshaghi
That error is because the lesionSegmentation.model file could not be found.  If you refer to the documentation page here and look at the "Quick Tour of Features and Use" you'll see a list of required inputs along with an image of the interface.  The Lesion Segmentation Model File is a required input and should be "set to the model file available with the tutorial."

Mark


-------- Original Message --------
Subject: Re: [slicer-users] Lupus Lesion Segmentation
Date: Wed, 25 May 2011 17:46:20 -0700 (PDT)
From: Joel Laxamana <[hidden email]>

Hello,

I've also run into this problem.  Has there been any updates on how to solve
this problem?  Also after the "Predict Lesions" run completes, the Status
says "Completed with errors".

Here is my complete error log. It may help if you saw the whole log:


Begin error log
==================================================

Type: Error
Time: Wed May 25 17:05:04 2011
Description: ERROR: In
/extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
line 1524
vtkCommandLineModuleLogic (0xa3337b0): Predict Lesions completed with errors




Type: Error
Time: Wed May 25 17:05:04 2011
Description: ERROR: In
/extra/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx,
line 1499
vtkCommandLineModuleLogic (0xa3337b0): Predict Lesions standard error:

Can't read lesionSegmentation.model




Type: Information
Time: Wed May 25 17:05:04 2011
Description: Predict Lesions standard output:

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Type: Information
Time: Wed May 25 16:51:31 2011
Description: Predict Lesions command line:

/home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/PredictLesions
--inputT1Volume
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeJ.nrrd
--inputT2Volume
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBA.nrrd
--inputFLAIRVolume
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBB.nrrd
--inputMaskVolume
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeF.nrrd
--inputPercentThreshold 12 --inputModelFile lesionSegmentation.model
--inputSVMModelFile svm.model --outputLesionMask
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBC.nrrd
--outputLesionProb
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBD.nrrd


Type: Information
Time: Wed May 25 16:51:28 2011
Description: CommandLineModule

Type: Information
Time: Wed May 25 16:51:28 2011
Description:
/home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/PredictLesions

Type: Information
Time: Wed May 25 16:51:28 2011
Description: Found CommandLine Module, target is

Type: Information
Time: Wed May 25 16:47:10 2011
Description: Joint Intensity Standardization completed without errors


Type: Information
Time: Wed May 25 16:47:10 2011
Description: Joint Intensity Standardization standard output:

<filter-end>
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</filter-end><filter-end>
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<filter-time>3.11466</filter-time>
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<filter-time>2.49927</filter-time>
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</filter-end><filter-end>
<filter-time>2.43317</filter-time>
</filter-end><filter-end>
<filter-time>3.09205</filter-time>
</filter-end>

Type: Information
Time: Wed May 25 16:46:52 2011
Description: Joint Intensity Standardization command line:

/home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/IntensityStandardize
--inputT1Mov
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeH.nrrd
--inputT2Mov
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeI.nrrd
--inputFLAIRMov
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeG.nrrd
--inputMovMask
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeF.nrrd
--inputT1Ref
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeD.nrrd
--inputT2Ref
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeE.nrrd
--inputFLAIRRef
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeC.nrrd
--inputRefMask
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeB.nrrd
--outputT1Mov
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeJ.nrrd
--outputT2
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBA.nrrd
--outputFlair
/home/vhasfclaxamj/Slicer3vhasfclaxamj/BACJH_vtkMRMLScalarVolumeNodeBB.nrrd


Type: Information
Time: Wed May 25 16:46:45 2011
Description: CommandLineModule

Type: Information
Time: Wed May 25 16:46:45 2011
Description:
/home/vhasfclaxamj/Slicer3vhasfclaxamj/16157/LesionSegmentationApplications/IntensityStandardize

Type: Information
Time: Wed May 25 16:46:45 2011
Description: Found CommandLine Module, target is

Type: Warning
Time: Wed May 25 16:42:16 2011
Description: Warning: In
/extra/pieper/slicer3/release/Slicer3/Libs/MRML/vtkMRMLCameraNode.cxx, line
449
vtkMRMLCameraNode (0xb89dbd0): SetActiveTag: vtkMRMLCameraNode1 found
another node vtkMRMLCameraNode1 with the tag vtkMRMLViewNode1

=========================================================================
End error log

Any feedback to get any resolution to this will be appreciated.

Thanks in advance,
Joel


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Re: Lupus Lesion Segmentation

Scully, Mark S
In reply to this post by Arman Eshaghi
The malloc error is due to the PredictLesions application requiring more
than four gigabytes of ram.  32 bit systems can only address four
gigabytes of ram so when run on a 32 bit version of slicer the malloc
error occurs.  An effort to refactor the PredictLesions program is
underway and one of the goals is to reduce the memory use and improve
multithreading support.

Mark

On 5/26/11 9:42 AM, "[hidden email]"
<[hidden email]> wrote:

>Date: Thu, 26 May 2011 09:51:11 +0530
>From: Madan Rao <[hidden email]>
>Subject: Re: [slicer-users] Lupus Lesion Segmentation
>To: [hidden email]
>Message-ID: <[hidden email]>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hello,
>
>It seems the error: malloc: *** mmap(size=67108864) failed (error code=12)
>is due to failed memory allocation to a variable PredictLesions which can
>be
>due to a simple code error or
>limited memory of the machine (which is more likely the cause).
>
>Hope this helps.*
>
>*AM Mohan Rao
>*
>*
>
>
>On Fri, Jul 16, 2010 at 10:52 PM, Arman Eshaghi
><[hidden email]>wrote:
>
>>Dear Jeremy (Bockholt),
>>
>>While I was running the tutorial data for Lupus White Matter Segmentation
>>in slicer 3.6, the following errors stop the analyzing process of
>>"Predict
>>Lesions" procedure.
>>
>>*ERROR: In
>>/Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineM
>>oduleLogic.cxx,
>>line 1497*
>>*vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions standard error:*
>>*
>>*
>>*PredictLesions(13725,0xa0814500) malloc: *** mmap(size=67108864) failed
>>(error code=12)*
>>**** error: can't allocate region*
>>**** set a breakpoint in malloc_error_break to debug*
>>*/Users/user/Slicer3user/13752/LesionSegmentationApplications/PredictLesi
>>ons:
>>exception caught !*
>>
>>
>>And the final error:
>>
>>
>>*ERROR: In
>>/Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineM
>>oduleLogic.cxx,
>>line 1522*
>>*vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions completed with
>>errors*
>>
>>
>>Thanks in advance,
>>Arman
>>
>>
>>_______________________________________________
>>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: Lupus Lesion Segmentation

Kikinis, Ron,M.D.
64 bit versions of slicer should be able to handle the larger memory
requirements, if the computer they are running on has the memory.

We have a 64 bit linux version

On 5/26/11 10:49 AM, Scully, Mark S wrote:

> The malloc error is due to the PredictLesions application requiring more
> than four gigabytes of ram.  32 bit systems can only address four
> gigabytes of ram so when run on a 32 bit version of slicer the malloc
> error occurs.  An effort to refactor the PredictLesions program is
> underway and one of the goals is to reduce the memory use and improve
> multithreading support.
>
> Mark
>
> On 5/26/11 9:42 AM, "[hidden email]"
> <[hidden email]>  wrote:
>
>> Date: Thu, 26 May 2011 09:51:11 +0530
>> From: Madan Rao<[hidden email]>
>> Subject: Re: [slicer-users] Lupus Lesion Segmentation
>> To: [hidden email]
>> Message-ID:<[hidden email]>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello,
>>
>> It seems the error: malloc: *** mmap(size=67108864) failed (error code=12)
>> is due to failed memory allocation to a variable PredictLesions which can
>> be
>> due to a simple code error or
>> limited memory of the machine (which is more likely the cause).
>>
>> Hope this helps.*
>>
>> *AM Mohan Rao
>> *
>> *
>>
>>
>> On Fri, Jul 16, 2010 at 10:52 PM, Arman Eshaghi
>> <[hidden email]>wrote:
>>
>>> Dear Jeremy (Bockholt),
>>>
>>> While I was running the tutorial data for Lupus White Matter Segmentation
>>> in slicer 3.6, the following errors stop the analyzing process of
>>> "Predict
>>> Lesions" procedure.
>>>
>>> *ERROR: In
>>> /Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineM
>>> oduleLogic.cxx,
>>> line 1497*
>>> *vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions standard error:*
>>> *
>>> *
>>> *PredictLesions(13725,0xa0814500) malloc: *** mmap(size=67108864) failed
>>> (error code=12)*
>>> **** error: can't allocate region*
>>> **** set a breakpoint in malloc_error_break to debug*
>>> */Users/user/Slicer3user/13752/LesionSegmentationApplications/PredictLesi
>>> ons:
>>> exception caught !*
>>>
>>>
>>> And the final error:
>>>
>>>
>>> *ERROR: In
>>> /Users/hayes/Slicer-3-6/Slicer3/Modules/CommandLineModule/vtkCommandLineM
>>> oduleLogic.cxx,
>>> line 1522*
>>> *vtkCommandLineModuleLogic (0x22a0d780): Predict Lesions completed with
>>> errors*
>>>
>>>
>>> Thanks in advance,
>>> Arman
>>>
>>>
>>> _______________________________________________
>>> 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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>
> ________________________________
> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
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--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
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