<div dir="ltr">Hi,<br><br>This is explained in length in the ITK guide, section 8.3.1 ("Direction of the Transform Mapping"). Yes, it is so confusing that they devoted a special section for it...<br><br>What you need to know is:<br>
1. The Registration module computes the transform from the FIXED image to the MOVING image. <br>2. If you set the INPUT image of the ResampleImageFilter to be the MOVING image, the OUTPUT image will be aligned to the FIXED image.<br>
<br>- Aviv<br><br><div class="gmail_quote">On Tue, Oct 7, 2008 at 9:28 AM, Lars Hegenbart <span dir="ltr"><<a href="mailto:Lars.Hegenbart@hs.fzk.de">Lars.Hegenbart@hs.fzk.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you for clarifying this!<br>
I am still confused about this. Is there a reason, why ITK does it this way?<br>
And how about a transform, determined by registration?<br>
Will it give me the appropriate transform for backward warping with ResampleImageFilter or do I have to invert the matrix somehow to apply the transform to my moving image, in order that it aligns with my fixed image?<br>
<br>
Thanks in advance for your hints!<br>
Lars<br>
<br>
Am 06.10.2008 um 17:55 schrieb Aviv Hurvitz:<div><div></div><div class="Wj3C7c"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
If I understand correctly, you expected your transform to be applied to the input image. This is called "forwards warping".<br>
<br>
In ITK, the ResampleImageFilter does "backwards warping": it uses the transform to go from the OUTPUT image to the INPUT image. In your case, the output pixel at 1,1,1 takes its color from 2,2,2, the output pixel at 2,2,2 takes its color from 4,4,4, etc. Your affine transform gives you a half-sized image.<br>
<br>
Hope that explains it.<br>
<br>
- Aviv<br>
<br>
<br>
<br>
On Mon, Oct 6, 2008 at 4:39 PM, Hegenbart, Lars <<a href="mailto:Lars.Hegenbart@hs.fzk.de" target="_blank">Lars.Hegenbart@hs.fzk.de</a>> wrote:<br>
Dear ITK-community,<br>
<br>
I am defining an affine transform with [2, 0, 0, 0, 2, 0, 0, 0, 2,<br>
0, 0, 0], basically a stretch of factor 2 in all 3 dimensions. I want to<br>
apply it to an input image to create an output image with same<br>
parameters (spacing, etc.). I end up getting an output which is scaled<br>
by a factor of 0.5 instead of 2. If I choose 0.5 in the diagonal of the<br>
matrix of the affine transform, I end up with the wanted result.<br>
It seems somehow to be inverted. What's wrong or is that normal?<br>
<br>
Thanks for any hints.<br>
<br>
Best regards<br>
Lars<br>
<br>
PS: here some relevant code parts:<br>
<br>
typedef itk::Image< unsigned char, Dimension > InputImageType;<br>
typedef itk::Image< unsigned char, Dimension > OutputImageType;<br>
InputImageType::Pointer i_image;<br>
OutputImageType::Pointer o_image;<br>
<br>
InputImageType::SpacingType spacing;<br>
spacing[0] = 6; //spacing along x<br>
spacing[1] = 6; //spacing along y<br>
spacing[2] = 6; //spacing along z<br>
i_image->SetSpacing(spacing);<br>
InputImageType::PointType origin;<br>
origin[0] = 0;<br>
origin[1] = 0;<br>
origin[2] = 0;<br>
i_image->SetOrigin(origin);<br>
InputImageType::SizeType size;<br>
size[0] = 100; // size along x<br>
size[1] = 100; // size along y<br>
size[2] = 100; // size along z<br>
<br>
typedef itk::AffineTransform< double, Dimension ><br>
<br>
TransformType;<br>
TransformType::Pointer transform;<br>
<br>
typedef TransformType::ParametersType ParametersType;<br>
const unsigned int numberOfParameters = transform-<br>
>GetNumberOfParameters();<br>
ParametersType parameters( numberOfParameters );<br>
parameters_affine[ 0]= 2;<br>
parameters_affine[ 1]= 0;<br>
parameters_affine[ 2]= 0;<br>
parameters_affine[ 3]= 0;<br>
parameters_affine[ 4]= 2;<br>
parameters_affine[ 5]= 0;<br>
parameters_affine[ 6]= 0;<br>
parameters_affine[ 7]= 0;<br>
parameters_affine[ 8]= 2;<br>
parameters_affine[ 9]= 0;<br>
parameters_affine[10]= 0;<br>
parameters_affine[11]= 0;<br>
transform->SetParameters( parameters);<br>
<br>
typedef itk::ResampleImageFilter< InputImageType,<br>
OutputImageType ><br>
FilterType;<br>
FilterType::Pointer filter = FilterType::New();<br>
filter->SetTransform(transform);<br>
<br>
typedef itk::NearestNeighborInterpolateImageFunction<<br>
InputImageType, double > InterpolatorType;<br>
InterpolatorType::Pointer interpolator =<br>
InterpolatorType::New();<br>
filter->SetInterpolator(interpolator);<br>
filter->SetDefaultPixelValue(0);<br>
<br>
filter->SetOutputSpacing(i_image->GetSpacing()); // same spacing<br>
like InputImage<br>
filter->SetOutputOrigin(i_image->GetOrigin()); // same like<br>
InputImage<br>
filter->SetSize(size); // same like InputImage<br>
filter->SetInput(i_image);<br>
<br>
o_image = filter->GetOutput();<br>
<br>
<br>
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</blockquote>
<br></div></div>
-------------------------------------------<br>
Dipl.-Ing. (FH) Lars Hegenbart<br>
<br>
Forschungszentrum Karlsruhe GmbH<br>
in der Helmholtz-Gemeinschaft<br>
Abteilung HS/KES<br>
Hermann-von-Helmholtz-Platz 1<br>
76344 Eggenstein-Leopoldshafen<br>
Germany<br>
<br>
Tel. +49-7247-82-3419<br><font color="#888888">
<a href="mailto:lars.hegenbart@kit.edu" target="_blank">lars.hegenbart@kit.edu</a><br>
<a href="http://www.hs-kes.de" target="_blank">http://www.hs-kes.de</a><br>
<br>
</font></blockquote></div><br></div>