Re: Fwd: Re: Robust Statistics Segmentation Memory Allocation Error

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Re: Fwd: Re: Robust Statistics Segmentation Memory Allocation Error

Gao, Yi
Hi Katherine,

Could I know the size of your data? There are two parameters,
"Intensity homogeneity" and "Boundary smoothness", could I know the
settings for them? I will try to think what may be happening there.

Sorry for jumping in late...


Best,
yi

On 05/16/2012 07:26 PM, Ron Kikinis wrote:

>
>
> -------- Original Message --------
> Subject: Re: [slicer-users] Robust Statistics Segmentation Memory
> Allocation Error
> Date: Wed, 16 May 2012 18:53:16 +0000
> From: Bloemker, Katherine H. <[hidden email]>
> To: [hidden email] <[hidden email]>
> CC: [hidden email] <[hidden email]>
>
>
>
> Thanks again Steve. I have tried the 64 bit build of Slicer 4.1. When I
> run RSS it runs (no errors) and says it’s completed, but does not update
> the label-map. It’s almost as if nothing happens, even though it tells
> me completed with no errors. Have you ever run into this problem with
> the 4.1 version? I am looking into the linux option right now.
>
> Katherine
>
> *From:*Steve Pieper [mailto:[hidden email]]
> *Sent:* Tuesday, May 15, 2012 3:57 PM
> *To:* Bloemker, Katherine H.
> *Cc:* [hidden email]
> *Subject:* Re: [slicer-users] Robust Statistics Segmentation Memory
> Allocation Error
>
> Hi Katherine -
>
> It looks like this ran out of memory too - with slicer3 on windows, the
> application itself only has a 32 bit address space so it doesn't behave
> well as the datasets get larger. Even on windows machines with more
> memory, the inherent 32 bit limit applies. In general we suggest a 64
> bit linux system with the 64 bit builds of slicer3 as a way to work with
> datasets that are too large for 32 bit systems. Do you have access to a
> 64 bit linux? If not it's easy to download a version that will run off
> an external disk or even a USB thumb drive that will work with most
> windows machines.
>
> By 'fresh' I meant that you try the segmenter just after starting slicer
> and loading only the one dataset you want to process.
>
> Another alternative is to get a 64 bit build of slicer 4.1, which also
> includes the RSS module, and run it on a 64 bit version of windows:
>
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/RobustStatisticsSegmenter
>
>
> -Steve
>
> On Tue, May 15, 2012 at 4:01 PM, Bloemker, Katherine H.
> <[hidden email] <mailto:[hidden email]>> wrote:
>
> Steve,
>
> Thank you for your response. I went ahead and tried a computer with more
> memory and it ran for a while (which was an improvement), but instead I
> got the following errors:
>
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
>
> 1658
>
> vtkCommandLineModuleLogic (0D6EBAC8): Robust Statistics Segmentation
> terminated with an unknown exception.
>
> ERROR: In c:\slicer-3-6\slicer3-lib\vtk\common\vtkDataArrayTemplate.txx,
> line 142
>
> vtkShortArray (137A9F60): Unable to allocate 29491200 elements of size 2
> bytes.
>
> ERROR: In ..\KWWidgets\vtkKWApplication.cxx, line 1301
>
> vtkSlicerApplication (04D35CB8): TclTk error: invalid command name
> "::EffectSWidget::drawEffect2"
>
> invalid command name "::EffectSWidget::drawEffect2"
>
> while executing
>
> "::EffectSWidget::drawEffect2 processDelayedAnnotation"
>
> ("after" script)
>
> Is this the same problem or something different? Also, when you say “try
> a fresh instance of slicer” what exactly do you mean?
>
> Thanks,
>
> Katherine
>
> *From:*Steve Pieper [mailto:[hidden email] <mailto:[hidden email]>]
> *Sent:* Tuesday, May 15, 2012 1:18 PM
> *To:* Bloemker, Katherine H.
> *Cc:* [hidden email] <mailto:[hidden email]>
> *Subject:* Re: [slicer-users] Robust Statistics Segmentation Memory
> Allocation Error
>
> Hi Katherine -
>
> Looks like you have run out of memory -- perhaps this image is larger
> than the previous ones you processed. Or perhaps you need to try with a
> fresh instance of slicer so that all memory is available. Or, for slicer
> 3.6, there are 64 bit linux binaries that should work for you.
>
> -Steve
>
> On Mon, May 14, 2012 at 4:41 PM, Bloemker, Katherine H.
> <[hidden email] <mailto:[hidden email]>> wrote:
>
> I am using the Robust Statistics Segmentation tool in Slicer 3.6 and am
> getting this error:
>
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
>
> 1647
>
> vtkCommandLineModuleLogic (0D9A0A80): Robust Statistics Segmentation
> terminated with an exception:
>
> itk::MemoryAllocationError (07A5C48C)
>
> Location: "double *__thiscall itk::ImportImageContainer<unsigned
> long,double>::AllocateElements(unsigned long) const"
>
> File:
> c:\cygwin\home\pieper\slicer3\release\slicer3-lib\insight\code\common\itkImportImageContainer.txx
>
>
> Line: 188
>
> Description: Failed to allocate memory for image.
>
> I have been using this tool for many other MR images with no problem,
> but this set keeps giving me this error. Any help would be greatly
> appreciated!
>
> Thanks,
>
> */Katherine H. Bloemker/*
>
> /Assistant Teaching Professor/
>
> /Department of Civil & Mechanical Engineering/
>
> /University of Missouri - Kansas City /
>
> 5110 Rockhill Road, 370B Flarsheim Hall
>
> Kansas City, MO 64110
>
> Phone: (816) 235-5639 <tel:%28816%29%20235-5639>
> E-mail: [hidden email] <mailto:[hidden email]>
>
>
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