Hi there,<br>I changed the images pixel type , to unsigned long , and almost solved the problem. Now in the first image pair the output image has values from 0-1318 and in the second image pair from 0-360, although it is not exactly the same.<br>
I had problem though in registering the images (through imageregistration8.cxx), because it didnt performed the right scaling correction.<br>Any help in that?<br>Thanks,<br>Giorgos<br><br><div class="gmail_quote">On Wed, Apr 2, 2008 at 1:40 PM, Giorgos Pichis <<a href="mailto:gpichis@gmail.com">gpichis@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Hi there,<br>I tried to solve the problem using RescaleIntensityImageFilter but it didnt fix the problem.<br>
The input image has greylevel values from 0-1362 and the output image from 0-220.<br>In another example input image had values from 0-376 and the output from 0-241. <br>
it seems that the writer by default writes the images in the scale 0-255, but rescaling to 0-512 or 0-1024 didnt fix the problem<br><br>Thanks , <br><font color="#888888">Giorgos</font><div><div></div><div class="Wj3C7c">
<br><br><div class="gmail_quote">On Tue, Apr 1, 2008 at 11:48 AM, Oliver Trebbe <<a href="mailto:otrebbe@uni-muenster.de" target="_blank">otrebbe@uni-muenster.de</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi there,<br>
I think i also have the same Problem.<br>
After filtering and resampling my greylevel scale reached form ~ -30000 to ~+30000.<br>
Im also a little bit confused (tried to change the input pixel types, but that didnt work:))<br>
But i also use the RescaleIntensityImageFilter.<br>
Maybe this can help solving the problem.<br>
<br>
Greatings<br>
Oliver<br>
<br>
<br>
Giorgos Pichis schrieb:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div>
Hi Luis,<br>
Here is the code I used. It is the example ResampleImageFilter5 with a change in the transform.<br>
The images were dicom mammography 3d images.<br>
The same problem appeared when I used .vtk 3d images . I didnt changed<br>
the input and output pixel type<br>
<br>
Thanks ,<br>
Giorgos<br>
<br>
<br>
#include "itkImage.h"<br>
#include "itkImageFileReader.h"<br>
#include "itkImageFileWriter.h"<br>
#include "itkResampleImageFilter.h"<br>
#include "itkLinearInterpolateImageFunction.h"<br>
#include "itkSimilarity3DTransform.h"<br>
<br>
int main( int argc, char * argv[] )<br>
{<br>
if( argc < 5 )<br>
{<br>
std::cerr << "Usage: " << std::endl;<br>
std::cerr << argv[0] << " inputImageFile outputImageFile degrees scale" << std::endl;<br>
return EXIT_FAILURE;<br>
}<br>
<br>
const unsigned int Dimension = 3;<br>
typedef unsigned char InputPixelType;<br>
typedef unsigned char OutputPixelType;<br>
<br>
typedef itk::Image< InputPixelType, Dimension > InputImageType;<br>
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;<br>
<br>
typedef itk::ImageFileReader< InputImageType > ReaderType;<br>
typedef itk::ImageFileWriter< OutputImageType > WriterType;<br>
<br>
ReaderType::Pointer reader = ReaderType::New();<br>
WriterType::Pointer writer = WriterType::New();<br>
<br>
reader->SetFileName( argv[1] );<br>
writer->SetFileName( argv[2] );<br>
typedef itk::Similarity3DTransform< double > TransformType;<br>
TransformType::Pointer transform = TransformType::New();<br>
<br>
typedef TransformType::ParametersType ParametersType;<br>
ParametersType parameters;<br>
double angleInDegrees = atof( argv[3] );<br>
double scale = atof( argv[4] );<br>
transform->SetScale(scale);<br>
typedef itk::ResampleImageFilter<<br>
InputImageType, OutputImageType > FilterType;<br>
<br>
FilterType::Pointer filter = FilterType::New();<br>
<br>
<br>
typedef itk::LinearInterpolateImageFunction<<br>
InputImageType, double > InterpolatorType;<br>
InterpolatorType::Pointer interpolator = InterpolatorType::New();<br>
filter->SetInterpolator( interpolator );<br>
<br>
filter->SetDefaultPixelValue( 0 );<br>
<br>
reader->Update();<br>
const InputImageType::SpacingType&<br>
spacing = reader->GetOutput()->GetSpacing();<br>
const InputImageType::PointType&<br>
origin = reader->GetOutput()->GetOrigin();<br>
InputImageType::SizeType size =<br>
reader->GetOutput()->GetLargestPossibleRegion().GetSize();<br>
<br>
filter->SetOutputOrigin( origin );<br>
filter->SetOutputSpacing( spacing );<br>
filter->SetSize( size );<br>
<br>
<br>
filter->SetInput( reader->GetOutput() );<br>
writer->SetInput( filter->GetOutput() );<br>
TransformType::InputPointType rotationCenter;<br>
rotationCenter[0] = origin[0] + spacing[0] * size[0] / 2.0;<br>
rotationCenter[1] = origin[1] + spacing[1] * size[1] / 2.0;<br>
rotationCenter[2] = origin[2] + spacing[2] * size[2] / 2.0;<br>
transform->SetCenter( rotationCenter );<br>
<br>
typedef TransformType::VersorType VersorType;<br>
typedef VersorType::VectorType VectorType;<br>
VersorType rotation;<br>
VectorType axis;<br>
axis[0]=0.0;<br>
axis[1]=0.0;<br>
axis[2]=1.0;<br>
double degreesToRadians = atan(1.0) / 45.0;<br>
const double angle = angleInDegrees * degreesToRadians;<br>
rotation.Set (axis, angle);<br>
transform->SetRotation( rotation );<br>
TransformType::OutputVectorType translation;<br>
<br>
translation[0] = 0.0;<br>
translation[1] = 0.0;<br>
translation[2] = 0.0;<br>
transform->SetTranslation (translation);<br>
<br>
filter->SetTransform( transform );<br>
<br>
try<br>
{<br>
writer->Update();<br>
}<br>
catch( itk::ExceptionObject & excep )<br>
{<br>
std::cerr << "Exception catched !" << std::endl;<br>
std::cerr << excep << std::endl;<br>
}<br>
return EXIT_SUCCESS;<br>
}<br>
<br>
<br></div></div><div>
On Fri, Mar 28, 2008 at 6:18 PM, Luis Ibanez <<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a> <mailto:<a href="mailto:luis.ibanez@kitware.com" target="_blank">luis.ibanez@kitware.com</a>>> wrote:<br>
<br>
Hi Giorgos,<br>
<br>
1) How different are the intensities of the output image ?<br>
<br>
2) What Transform are you using ?<br>
<br>
3) What interpolator are you using ?<br>
<br>
4) What image type did you defined for the input ?<br>
<br>
5) What image type did you defined for the output ?<br>
<br>
6) What is the modality of the input image ?<br>
<br>
...<br>
<br>
7) Please post your code to the list.<br>
<br>
<br>
Thanks<br>
<br>
<br>
Luis<br>
<br>
<br>
-----------------------<br>
Giorgos Pichis wrote:<br>
> Hi there,<br>
> I tried to resample a 3d image (.vtk) with a transformation,<br>
> but the output image ( writer->SetInput(filter->GetOutput() ); )<br>
> had different intensity values than the input image.<br>
> Do you know what might be the problem?<br>
> Thanks<br>
><br>
><br>
><br>
------------------------------------------------------------------------<br>
><br>
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</div></blockquote>
<br>
</blockquote></div><br>
</div></div></blockquote></div><br>