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

Stephen Aylward stephen.aylward at kitware.com
Mon Dec 20 10:36:22 EST 2010


Hi,

Currently, Slicer is only available in 32-bit versions.    So, while
your machine has 12 gigs, Slicer can only reference ~3gigs at this
time.

We will release a 64bit version very soon (by end of January).

In the meantime, you may want to try to reduce the size of your image
by subsampling it.

s

On Mon, Dec 20, 2010 at 10:25 AM, Boettcher, PD Dr. Peter
<Boettcher at kleintierklinik.uni-leipzig.de> 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.cxx,
> 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.cxx,
> 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_vtkMRMLLinearTransformNodeE.txt
> --outputtransform
> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLBSplineTransformNodeB.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_vtkMRMLLinearTransformNodeE.txt
>     FixedImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode1
>     MovingImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode2
>     OutputTransform:
> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLBSplineTransformNodeB.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_vtkMRMLLinearTransformNodeE.txt
>     FixedImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode1
>     MovingImageFileName: slicer:037BB188#vtkMRMLScalarVolumeNode2
>     OutputTransform:
> C:/Users/braeuer/AppData/Local/Temp/1/Slicer3/CGHC_vtkMRMLBSplineTransformNodeB.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
>
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>



-- 

==============================
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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