[slicer-users] Memory error when using B-spline registration

Stephen Aylward stephen.aylward at kitware.com
Mon Dec 20 10:48:00 EST 2010


Depending on the BSpline module - there may also be an advanced option
to conserve memory - it takes longer to run, but the memory
requirement is nearly cut in half.

s

On Mon, Dec 20, 2010 at 10:46 AM, Boettcher, PD Dr. Peter
<Boettcher at kleintierklinik.uni-leipzig.de> wrote:
> Thank you!
>
> We are running a 32-bit version on Windows. Therefore we will have to wait for the 64-bit windows version coming up next year. If we use a down sampled volume for registration, could we apply the calculated matrix to the original volume? Croping is not an option as our roi already fits well into the volume.
>
>
> Regards, Peter.
>
> -----Ursprüngliche Nachricht-----
> Von: Ron Kikinis [mailto:kikinis at bwh.harvard.edu]
> Gesendet: Montag, 20. Dezember 2010 16:39
> An: Boettcher, PD Dr. Peter
> Betreff: Fwd: Re: [slicer-users] Memory error when using B-spline registration
>
>
>
> -------- Original Message --------
> Subject: Re: [slicer-users] Memory error when using B-spline registration
> Date: Mon, 20 Dec 2010 10:38:14 -0500
> From: Ron Kikinis <kikinis at bwh.harvard.edu>
> Reply-To: kikinis at bwh.harvard.edu
> To: slicer-users at bwh.harvard.edu
>
> Hi,
>
> What version of Slicer are you using and on what platform? If you are running a 32 bit version of Slicer, the memory available to slicer is slightly less than 2GB.
>
> If you compile yourself, you can compile a 64bit version. If you are using the precompiled downloads, then we make a 64 bit version available on Linux. We are working of other 64bit versions, but I do not expect them for several weeks.
>
> Ron
>
> On 12/20/10 10:25 AM, Boettcher, PD Dr. Peter wrote:
>> We use slicer and B-spline registration for non-rigid registration of
>> CT data. Unfortunately when increasing the grid size (>7) an error occurs.
>> The mashine slicer is running has 12 GB ram, but slicer refers to
>> insufficient memory.
>> Please see the posted error log message for further details.
>> Any comment would be highly appreciate!
>> Regards, Peter.
>> Type: Error
>> Time: 12/20/10 16:14:19
>> Description: ERROR: In
>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.c
>> xx, line
>> 1622
>> vtkCommandLineModuleLogic (0C7E9E90): Fast Nonrigid BSpline
>> registration standard error:
>> ExceptionObject caught !
>> itk::ExceptionObject (078BB060)
>> Location: "float *__thiscall itk::ImportImageContainer<unsigned
>> long,float>::AllocateElements(unsigned long) const"
>> File:
>> c:\slicer-3-6\slicer3-lib\insight\code\common\itkImportImageContainer.
>> txx
>> Line: 188
>> Description: Failed to allocate memory for image.
>>
>> Type: Error
>> Time: 12/20/10 16:14:19
>> Description: ERROR: In
>> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.c
>> xx, line
>> 1671
>> vtkCommandLineModuleLogic (0C7E9E90): Fast Nonrigid BSpline
>> registration returned 1 which probably indicates an error.
>>
>> Type: Information
>> Time: 12/20/10 16:14:18
>> Description: Fast Nonrigid BSpline registration command line:
>> slicer:6C94EAE0 --processinformationaddress 109C7F10 --iterations 20
>> --gridSize 10 --histogrambins 100 --spatialsamples 50000
>> --maximumDeformation 1 --default 0 --initialtransform
>> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLLinearTransf
>> ormNodeE.txt
>> --outputtransform
>> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLBSplineTrans
>> formNodeB.txt --resampledmovingfilename
>> slicer:037BB188#vtkMRMLScalarVolumeNode3
>> slicer:037BB188#vtkMRMLScalarVolumeNode1
>> slicer:037BB188#vtkMRMLScalarVolumeNode2
>>
>> Type: Information
>> Time: 12/20/10 16:14:19
>> Description: Fast Nonrigid BSpline registration standard output:
>> Command Line Arguments
>> Iterations: 20
>> gridSize: 10
>> HistogramBins: 100
>> SpatialSamples: 50000
>> ConstrainDeformation: 0
>> MaximumDeformation: 1
>> DefaultPixelValue: 0
>> InitialTransform:
>> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLLinearTransf
>> ormNodeE.txt
>> FixedImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode1
>> MovingImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode2
>> OutputTransform:
>> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLBSplineTrans
>> formNodeB.txt
>> ResampledImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode3
>> echoSwitch: 1
>> xmlSwitch: 0
>> processInformationAddressString: 109C7F10
>> returnParameterFile:
>> Command Line Arguments
>> Iterations: 20
>> gridSize: 10
>> HistogramBins: 100
>> SpatialSamples: 50000
>> ConstrainDeformation: 0
>> MaximumDeformation: 1
>> DefaultPixelValue: 0
>> InitialTransform:
>> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLLinearTransf
>> ormNodeE.txt
>> FixedImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode1
>> MovingImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode2
>> OutputTransform:
>> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLBSplineTrans
>> formNodeB.txt
>> ResampledImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode3
>> echoSwitch: 1
>> xmlSwitch: 0
>> processInformationAddressString: 109C7F10
>> returnParameterFile:
>> Centering transform: AffineTransform (134601A8) RTTI typeinfo: class
>> itk::AffineTransform<double,3> Reference Count: 1 Modified Time: 4811
>> Debug: Off
>> Observers:
>> none
>> Matrix:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>> Offset: [1.06581e-014, 1.06581e-014, -7.10543e-015]
>> Center: [-3.55271e-015, -3.55271e-015, 0]
>> Translation: [1.06581e-014, 1.06581e-014, -7.10543e-015]
>> Inverse:
>> 1 0 0
>> 0 1 0
>> 0 0 1
>> Singular: 0
>> Initial transform: AffineTransform (13460060) RTTI typeinfo: class
>> itk::AffineTransform<double,3> Reference Count: 5 Modified Time: 3847
>> Debug: Off
>> Observers:
>> none
>> Matrix:
>> 1 -0 0
>> -0 0.979925 0.199368
>> 0 -0.199368 0.979925
>> Offset: [0, -1.8943, 7.32471]
>> Center: [0, 0, 0]
>> Translation: [0, -1.8943, 7.32471]
>> Inverse:
>> 1 0 0
>> 0 0.979924 -0.199368
>> 0 0.199368 0.979924
>> Singular: 0
>> Starting Registration
>>
>> Type: Information
>> Time: 12/20/10 16:14:18
>> Description: Found SharedObject Module
>> Type: Information
>> Time: 12/20/10 16:14:18
>> Description: SharedObjectModule
>> ------------------------------------
>> Peter Böttcher, PD, Dr med vet, DipECVS European Veterinary Specialist
>> in Surgery Fachtierarzt für Kleintierchirurgie Klinik für Kleintiere
>> Universität Leipzig An den Tierkliniken 23
>> D-04103 Leipzig (Germany)
>> Tel: +49-341-9738700
>> Fax: +49-341-9738799
>> email: boettcher at kleintierklinik.uni-leipzig.de
>> <mailto:boettcher at kleintierklinik.uni-leipzig.de>
>>
>>
>>
>> _______________________________________________
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>> To unsubscribe: send email to
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>> subject
>
> --
> 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
>



-- 

==============================
Stephen R. Aylward, Ph.D.
Director of Medical Imaging Research
Kitware, Inc. - North Carolina Office
http://www.kitware.com
stephen.aylward (Skype)
(919) 969-6990 x300



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