[Insight-users] transform an image problem

[Luis Ibanez]

Hi Moti,

Did you set the Center of rotation
 in the Affine Transform ?

---

and yet, a better solution,

you could use directly ICP implementation in ITK,
and fee it with points that have been harvested
using the:

                   IndexToPhysicalPoint()

method of the itkImages.

In that way you will be sure of using points
that are really in the same coordinate system
as the images.

It is quite likely that the point coordinates
that you used as input for the VTK ICP
algorithm, do not map to the locations
that you are expecting in the ITK images.


Also, keep in mind that VTK and ITK
have a reflection in the coordinates of
the Y axis... this may also be playing
here...



    Regards,


         Luis


------------------------------------------------------
On Tue, Sep 28, 2010 at 10:09 AM, Moti Freiman <freiman at cs.huji.ac.il>wrote:

> Hi,
> Thanks for the fast answer.
> I added the direction code as you can see below. Problem still not solved
> yet.
> I think that I handle the origin, and orientation well now.
> Any other suggestion?
> Thanks,
> Moti
>
>
>
> resampler->SetOutputSpacing( fixedImage->GetSpacing() );
> resampler->SetSize(  fixedImage->GetLargestPossibleRegion().GetSize() );
> resampler->SetOutputOrigin( fixedImage->GetOrigin());
> resampler->SetOutputDirection(movingImage->GetDirection());
>
> On Tue, Sep 28, 2010 at 9:27 AM, Vincent Magnotta
> <vincent-magnotta at uiowa.edu> wrote:
> > Moti,
> >
> > The number one reason for this type of error is not correctly handling
> the
> > origin and orientation in the images. Just quickly looking at the code,
> you
> > should also set the direction of the output image.
> >
> > Vince
> >
> >
> >
> > On 9/28/10 8:22 AM, "Moti Freiman" <freiman at cs.huji.ac.il> wrote:
> >
> >> Hi All,
> >> I have an affine transformation that I produced using the ICP
> >> algorithm as implemented in VTK.
> >> Now I want to transfer the original moving image to the coordinates of
> >> the fixed one.
> >>
> >> I wrote a simple ITK based application, that read the images and the
> >> transform, and apply the trasnform to the moving image.
> >> However, It seems that I got an empty image (with default value),
> >> although the transformation of the surfaces using VTK works well.
> >> I tested the transformation by transforming several points using both
> >> ITK transform and the VTK transform, and the points transffered
> >> indentically.
> >> Does any one has an idea, some expirience with that problem.
> >>
> >> The code is attached bellow
> >> Best,
> >> Moti
> >>
> >>
> >>
> >>
> >> --------------------------------- ITK based affine image
> >> transformation -------------------------------------------
> >>
> >>         // declare the affine transfrom
> >> typedef itk::AffineTransform <double,Dimension> itkAffineTransformType;
> >> itkAffineTransformType::Pointer trans = itkAffineTransformType::New();
> >> trans->SetIdentity();
> >>
> >> // read transform params from file
> >> std::fstream transFile;
> >> transFile.open (inputReferenceToPatientTransformFileName.c_str(),
> >> std::ios::in);
> >> int numOfElements = Dimension*Dimension;
> >>
> >> itkAffineTransformType::MatrixType matrix;
> >> itkTranslationTransformType::OutputVectorType translation;
> >>
> >> for (int i=0;i<Dimension;++i)
> >> {
> >> for (int j=0;j<Dimension;++j)
> >> {
> >> transFile >> matrix(i,j);
> >> }
> >> }
> >> dout << "end to read matrix" << std::endl;
> >> for (int i=0;i<Dimension;++i)
> >> {
> >> transFile >> translation[i];
> >> translation[i]  = -translation[i];
> >>
> >> }
> >>
> >> transFile.close();
> >>
> >>
> >>
> >> trans->SetMatrix( matrix );
> >> trans->SetOffset(translation);
> >>
> >>         // transform some point for testing purpose
> >> dout << trans << std::endl;
> >> itkAffineTransformType::InputPointType inPoint;
> >> inPoint[0] = 1;  inPoint[1] = 1; inPoint[2] = 1;
> >> itkAffineTransformType::OutputPointType outPoint =
> >> trans->TransformPoint(inPoint);
> >> dout << outPoint[0] << ", " << outPoint[1] << ", " << outPoint[2] <<
> >> std::endl;
> >>
> >>
> >>         // resample the moving image
> >>         typedef itk::ResampleImageFilter< LabelsImageType,
> >> LabelsImageType > ResampleFilterType;
> >> ResampleFilterType::Pointer resampler = ResampleFilterType::New();
> >>
> >>
> >>
> >> typedef itk::NearestNeighborInterpolateImageFunction<LabelsImageType,
> >> double> InterpolatorType;
> >> InterpolatorType::Pointer interpolator = InterpolatorType::New();
> >> resampler->SetInterpolator( interpolator );
> >> resampler->SetTransform( trans );
> >> resampler->SetDefaultPixelValue(100);
> >> resampler->SetOutputSpacing( fixedImage );
> >> resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
> >> resampler->SetOutputOrigin( fixedImage->GetOrigin());
> >> resampler->SetInput (movingImage);
> >>
> >>
> >> resampler->Update();
> >>
> >>
> >> ------------------------------------------ end of code
> >> --------------------------------------------------------------
> >
> > ----------------------
> > Associate Professor
> > Department of Radiology
> > 0453-D JCP
> > 200 Hawkins Drive
> > Iowa City, IA 52242
> > E-mail: vincent-magnotta at uiowa.edu
> > Phone: 319-356-8255 Fax: 319-353-6275
> > Website: http://www.radiology.uiowa.edu
> >
> >
> >
> >
>
>
>
> --
> __
> Moti Freiman, Postdoctoral Associate,
> Harvard Medical School.
> Research Fellow,
> Computational Radiology Laboratory.
> Dept. of Radiology, Children's hospital,
> 300 Longwood Ave. Boston, MA 02115.
>
> Lab website: http://crl.med.harvard.edu
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