[Insight-users] output image with different grey levels
Giorgos Pichis
gpichis at gmail.com
Wed Apr 2 09:47:47 EDT 2008
Hi there,
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.
I had problem though in registering the images (through
imageregistration8.cxx), because it didnt performed the right scaling
correction.
Any help in that?
Thanks,
Giorgos
On Wed, Apr 2, 2008 at 1:40 PM, Giorgos Pichis <gpichis at gmail.com> wrote:
>
> Hi there,
> I tried to solve the problem using RescaleIntensityImageFilter but it
> didnt fix the problem.
> The input image has greylevel values from 0-1362 and the output image from
> 0-220.
> In another example input image had values from 0-376 and the output from
> 0-241.
> 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
>
> Thanks ,
> Giorgos
>
>
> On Tue, Apr 1, 2008 at 11:48 AM, Oliver Trebbe <otrebbe at uni-muenster.de>
> wrote:
>
> > Hi there,
> > I think i also have the same Problem.
> > After filtering and resampling my greylevel scale reached form ~ -30000
> > to ~+30000.
> > Im also a little bit confused (tried to change the input pixel types,
> > but that didnt work:))
> > But i also use the RescaleIntensityImageFilter.
> > Maybe this can help solving the problem.
> >
> > Greatings
> > Oliver
> >
> >
> > Giorgos Pichis schrieb:
> >
> > > Hi Luis,
> > > Here is the code I used. It is the example ResampleImageFilter5 with a
> > > change in the transform.
> > > The images were dicom mammography 3d images.
> > > The same problem appeared when I used .vtk 3d images . I didnt changed
> > > the input and output pixel type
> > >
> > > Thanks ,
> > > Giorgos
> > >
> > >
> > > #include "itkImage.h"
> > > #include "itkImageFileReader.h"
> > > #include "itkImageFileWriter.h"
> > > #include "itkResampleImageFilter.h"
> > > #include "itkLinearInterpolateImageFunction.h"
> > > #include "itkSimilarity3DTransform.h"
> > >
> > > int main( int argc, char * argv[] )
> > > {
> > > if( argc < 5 )
> > > {
> > > std::cerr << "Usage: " << std::endl;
> > > std::cerr << argv[0] << " inputImageFile outputImageFile degrees
> > > scale" << std::endl;
> > > return EXIT_FAILURE;
> > > }
> > >
> > > const unsigned int Dimension = 3;
> > > typedef unsigned char InputPixelType;
> > > typedef unsigned char OutputPixelType;
> > >
> > > typedef itk::Image< InputPixelType, Dimension > InputImageType;
> > > typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> > >
> > > typedef itk::ImageFileReader< InputImageType > ReaderType;
> > > typedef itk::ImageFileWriter< OutputImageType > WriterType;
> > >
> > > ReaderType::Pointer reader = ReaderType::New();
> > > WriterType::Pointer writer = WriterType::New();
> > >
> > > reader->SetFileName( argv[1] );
> > > writer->SetFileName( argv[2] );
> > > typedef itk::Similarity3DTransform< double > TransformType;
> > > TransformType::Pointer transform = TransformType::New();
> > >
> > > typedef TransformType::ParametersType ParametersType;
> > > ParametersType parameters;
> > > double angleInDegrees = atof( argv[3] );
> > > double scale = atof( argv[4] );
> > > transform->SetScale(scale);
> > > typedef itk::ResampleImageFilter<
> > > InputImageType, OutputImageType > FilterType;
> > >
> > > FilterType::Pointer filter = FilterType::New();
> > >
> > >
> > > typedef itk::LinearInterpolateImageFunction<
> > > InputImageType, double > InterpolatorType;
> > > InterpolatorType::Pointer interpolator = InterpolatorType::New();
> > > filter->SetInterpolator( interpolator );
> > >
> > > filter->SetDefaultPixelValue( 0 );
> > >
> > > reader->Update();
> > > const InputImageType::SpacingType&
> > > spacing = reader->GetOutput()->GetSpacing();
> > > const InputImageType::PointType&
> > > origin = reader->GetOutput()->GetOrigin();
> > > InputImageType::SizeType size =
> > > reader->GetOutput()->GetLargestPossibleRegion().GetSize();
> > >
> > > filter->SetOutputOrigin( origin );
> > > filter->SetOutputSpacing( spacing );
> > > filter->SetSize( size );
> > >
> > >
> > > filter->SetInput( reader->GetOutput() );
> > > writer->SetInput( filter->GetOutput() );
> > > TransformType::InputPointType rotationCenter;
> > > rotationCenter[0] = origin[0] + spacing[0] * size[0] / 2.0;
> > > rotationCenter[1] = origin[1] + spacing[1] * size[1] / 2.0;
> > > rotationCenter[2] = origin[2] + spacing[2] * size[2] / 2.0;
> > > transform->SetCenter( rotationCenter );
> > >
> > > typedef TransformType::VersorType VersorType;
> > > typedef VersorType::VectorType VectorType;
> > > VersorType rotation;
> > > VectorType axis;
> > > axis[0]=0.0;
> > > axis[1]=0.0;
> > > axis[2]=1.0;
> > > double degreesToRadians = atan(1.0) / 45.0;
> > > const double angle = angleInDegrees * degreesToRadians;
> > > rotation.Set (axis, angle);
> > > transform->SetRotation( rotation );
> > > TransformType::OutputVectorType translation;
> > >
> > > translation[0] = 0.0;
> > > translation[1] = 0.0;
> > > translation[2] = 0.0;
> > > transform->SetTranslation (translation);
> > >
> > > filter->SetTransform( transform );
> > >
> > > try
> > > {
> > > writer->Update();
> > > }
> > > catch( itk::ExceptionObject & excep )
> > > {
> > > std::cerr << "Exception catched !" << std::endl;
> > > std::cerr << excep << std::endl;
> > > }
> > > return EXIT_SUCCESS;
> > > }
> > >
> > >
> > > On Fri, Mar 28, 2008 at 6:18 PM, Luis Ibanez <luis.ibanez at kitware.com<mailto:
> > > luis.ibanez at kitware.com>> wrote:
> > >
> > > Hi Giorgos,
> > >
> > > 1) How different are the intensities of the output image ?
> > >
> > > 2) What Transform are you using ?
> > >
> > > 3) What interpolator are you using ?
> > >
> > > 4) What image type did you defined for the input ?
> > >
> > > 5) What image type did you defined for the output ?
> > >
> > > 6) What is the modality of the input image ?
> > >
> > > ...
> > >
> > > 7) Please post your code to the list.
> > >
> > >
> > > Thanks
> > >
> > >
> > > Luis
> > >
> > >
> > > -----------------------
> > > Giorgos Pichis wrote:
> > > > Hi there,
> > > > I tried to resample a 3d image (.vtk) with a transformation,
> > > > but the output image ( writer->SetInput(filter->GetOutput() );
> > > )
> > > > had different intensity values than the input image.
> > > > Do you know what might be the problem?
> > > > Thanks
> > > >
> > > >
> > > >
> > >
> > > ------------------------------------------------------------------------
> > > >
> > > > _______________________________________________
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> > >
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
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> > >
> > >
> >
> >
>
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