[Insight-users] VersorRigid3DTransform Scaling Problem

[Luis Ibanez]

Hi Tahir,

It seems that there is a confusion in your use of the output spacing.

You are allowed to use *any* spacing for resampling the moving image,
the spacing that is usually more appropriate is the spacing of the
fixed image because it is common to overlap the resampled moving
image into the fixed image.

The problem that you are observing seems to be the consequence
of using an inappropriate viewer or a poor file format for storing
your images.

You *DO NOT* need the spacing to the isotropic, and you *DO NOT*
need rotations to be limited to 90 degrees in order to have the
resampling working properly.

In practice, what you should probably do is to simply use the
spacing of the Fixed image, and to make sure that you use a viewer
that supports pixel spacing. (e.g. VTK).

That being said. From the description at the top of your email,
it seems that what you want to do is to simply rotate your image
by 90 degrees.  This is more a case of Axis Permutation than a
case for a full image resampling.


You probably want to consider the PermuteAxesImageFilter:

http://www.itk.org/Insight/Doxygen/html/classitk_1_1PermuteAxesImageFilter.html




   Regards,


      Luis




----------------------
Tahir Mansoori wrote:
> Hi,
> 
> I am using VersorRigid3DTransform to rotate 3D volume. The physical
> spacing is 212 X 212 X 392 um. I am rotating volume around Y-Axis by
> 90 degrees.
> 
> This is a very simple case because input spacing 212 X 212 X 392 um
> will be changed to output spacing of 392X212X212.
> 
> But if I rotate volume first around Z axis 45 degrees and then around
> X axis 65 degrees, then output spacing need to be calculated by
> applying this transform to a cube having dimensions 212 X 212 X 392
> um.
> 
>  TransformType::Pointer  transform = TransformType::New();
>  typedef TransformType::VersorType  VersorType;
>  typedef VersorType::VectorType     VectorType;
> 
>  VersorType     rotation;
>  VectorType     axis;
> 
>  axis[0] = 0;
>  axis[1] = 1;
>  axis[2] = 0;
> 
>  const double angle = 1.571; // 90 degrees
> 
>  rotation.Set(  axis, angle  );
> 
>  transform->SetRotation( rotation );
> 
>  ResampleFilterType::Pointer resampler = ResampleFilterType::New();
> 
>  resampler->SetTransform( transform );
>  resampler->SetInput( fixedImageReader->GetOutput() );
> 
>  FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
> 
>  resampler->SetSize(    fixedImage->GetLargestPossibleRegion().GetSize() );
>  resampler->SetOutputOrigin(  fixedImage->GetOrigin() );
> ** resampler->SetOutputSpacing( fixedImage->GetSpacing() );
>  resampler->SetDefaultPixelValue( 255 );
> 
> The line marked with ** does not work if spacing along all dimensions
> is not equal or rotation angles are not multiple of pi/2.
> 
> If there any function or transform in itk to calculate output scaling.
> 
> Tahir Mansoori
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