[Insight-users] Vital DICOM information/tags when registering images?

[Patrik Brynolfsson]

Hello Bill, thanx for answering!

The filter I use are:
Registration part (same for both cases):

itkImageRegistrationMethod
itkMattesMutualInformationImageToImageMetric
itkLinearInterpolateImageFunction
itkVersorRigid3DTransform
itkVersorRigid3DTransformOptimizer
itkCenteredTransformInitializer

Reading images from memory:

itkImportImageFilter
itkChangeInformationImageFilter

Reading images from DICOM:

itkImageSeriesReader
itkGDCMImageIO
itkGDCMSeriesFileNames

*The code to read images from memory is:*

  typedef itk::ImportImageFilter<PixelType,Dimension> ImportFilterType;
  ImportFilterType::Pointer fixedImageReader = ImportFilterType::New();
  ImportFilterType::Pointer movingImageReader = ImportFilterType::New();

  const mwSize*   dimsFix = mxGetDimensions(prhs[0]);
  const mwSize*   dimsMov = mxGetDimensions(prhs[1]);

  ImportFilterType::SizeType sizeFix;
  ImportFilterType::SizeType sizeMov;
  sizeFix[0] = dimsFix[0];
  sizeFix[1] = dimsFix[1];
  sizeFix[2] = dimsFix[2];

  sizeMov[0] = dimsMov[0];
  sizeMov[1] = dimsMov[1];
  sizeMov[2] = dimsMov[2];

  ImportFilterType::IndexType start;
  start.Fill( 0 );
  ImportFilterType::RegionType regionFix;
  regionFix.SetIndex( start );
  regionFix.SetSize(  sizeFix  );
  ImportFilterType::RegionType regionMov;
  regionMov.SetIndex( start );
  regionMov.SetSize(  sizeMov  );
  fixedImageReader->SetRegion( regionFix );
  movingImageReader->SetRegion(regionMov );

  //Import image from memory, passed from MATLAB
  fixedImageReader->SetImportPointer((PixelType*)mxGetData(prhs[0]),mxGetNumberOfElements(prhs[0]),false);
  movingImageReader->SetImportPointer((PixelType*)mxGetData(prhs[1]),mxGetNumberOfElements(prhs[1]),false);
  fixedImageReader->Update();
  movingImageReader->Update();

*...and the code to set the relevant info is:*

  double *fixedSpacingInput    = mxGetPr(prhs[2]);
  double *movingSpacingInput = mxGetPr(prhs[3]);

  double *fixedOrientationInput = mxGetPr(prhs[4]);
  double *movingOrientationInput = mxGetPr(prhs[5]);

  double *fixedOriginInput = mxGetPr(prhs[6]);
  double *movingOriginInput = mxGetPr(prhs[7]);

  **Code for casting input to correct types are skipped, not important for
this question**

  typedef itk::ChangeInformationImageFilter< FixedImageType >
ChangeInfoType;
  ChangeInfoType::Pointer changeFixedInfo = ChangeInfoType::New();
  ChangeInfoType::Pointer changeMovingInfo = ChangeInfoType::New();

  changeFixedInfo->SetInput(fixedImageReader->GetOutput());
  changeMovingInfo->SetInput(movingImageReader->GetOutput());

  changeFixedInfo->SetOutputSpacing(fixedSpacing);
  changeMovingInfo->SetOutputSpacing(movingSpacing);
  changeFixedInfo->SetChangeSpacing(true);
  changeMovingInfo->SetChangeSpacing(true);

  changeFixedInfo->SetOutputDirection(fixedOrientation);
  changeMovingInfo->SetOutputDirection(movingOrientation);
  changeFixedInfo->SetChangeDirection(true);
  changeMovingInfo->SetChangeDirection(true);

  changeFixedInfo->SetOutputOrigin(fixedOrigin);
  changeMovingInfo->SetOutputOrigin(movingOrigin);
  changeFixedInfo->SetChangeOrigin(true);
  changeMovingInfo->SetChangeOrigin(true);

  changeFixedInfo->Update();
  changeMovingInfo->Update();

  registration->SetFixedImage(    changeFixedInfo->GetOutput()    );
  registration->SetMovingImage(   changeMovingInfo->GetOutput()   );
  registration->SetFixedImageRegion(
changeFixedInfo->GetOutput()->GetBufferedRegion()
);

As a check I print the origin, spacing and direction for the images and they
are identical to when reading from DICOM files. I read the DICOM series just
as described in chapter 7.12 in the ITK manual.

Any ideas to what might be wrong here?

Thanks in advance!

//Patrik Brynolfsson



2009/9/16 Bill Lorensen <bill.lorensen at gmail.com>

> You should get the same answers. Exactly what filters are you using in
> each of the cases. I can't tell from your description.
>
> Bill
>
> On Tue, Sep 15, 2009 at 4:38 PM, Patrik Brynolfsson
> <patrik.brynolfsson at gmail.com> wrote:
> > Hello,
> > I'm working on a Matlab mex-implementation of an ITK registration. This
> > means that instead of loading the images from files I will load them from
> > memory as 3D matrices. All the DICOM information needs to be passed to
> ITK
> > from Matlab as well, and this is where my problems begin. The information
> > that I thought was essential for a correct registration is:
> > * Origin
> > * Spacing
> > * Direction
> > I set these using the "ChangeInformationImageFilter" and it is working;
> the
> > images have the origin, spacing and directional cosines that are assigned
> to
> > them, and they are the same as if the dicom images were loaded from
> files.
> > However, the result of the registration is different from that when
> loading
> > the images from files, with all other components set the same, (of course
> I
> > reinitialize the seed). Not by much, but they should be exactly the same!
> I
> > use Mattes mutual information metric, linear interpolation, Versor rigid
> 3D
> > transform and the accompanying Versor rigid 3D optimizer together with
> the
> > "CenteredTransformInitializer".
> > I know that the difference in results are due to the way I read the data.
> If
> > I change the input from memory to reading the dicom files I get the same
> > result as with a stand-alone .exe-application, so this is where the error
> > is.
> > Does anyone have any idea as to what other information I need to pass
> from
> > matlab to get identical results?
> > Thanks in advance
> > --
> > Patrik Brynolfsson
> >
> >
> >
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>



-- 
Patrik Brynolfsson
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20090916/f0f7f731/attachment-0001.htm>