[Insight-users] Boundary problem when resampling?

[stan]

Hi again Bill

I would like to understand what the flag
ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY does ...

Could you explain what's the difference with respect to physical
coordinates when this flag is ON and OFF?

Thanks !

stan



Le lundi 16 novembre 2009 à 09:47 +0100, stan a écrit :
> Thanks a lot Bill, now it works correctly.
> 
> stan
> 
> 
> Le vendredi 13 novembre 2009 à 11:12 -0500, Bill Lorensen a écrit :
> > Statring in 3.16 we made the default for
> > ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY to be ON.
> > 
> > In 3.14 the default was OFF. If you have not turned this on in your
> > build, can you try that.
> > 
> > Bill
> > 
> > On Fri, Nov 13, 2009 at 11:02 AM, stan <stan.oubel at gmail.com> wrote:
> > > I'm using itk 3.14 ...
> > >
> > >
> > > Le vendredi 13 novembre 2009 à 10:52 -0500, Bill Lorensen a écrit :
> > >> What version of itk are you using?
> > >>
> > >> On Fri, Nov 13, 2009 at 10:13 AM, stan <stan.oubel at gmail.com> wrote:
> > >> > Dear all,
> > >> >
> > >> > I'm using the ITK resampling filter to upscale 3D images
> > >> > (BSplineInterpolateImageFunction).
> > >> >
> > >> > I encountered two problems with this filter:
> > >> >
> > >> > - there is a misregistration between high-resolution images and
> > >> > resampled low-resolution images. To correct that, I modified the origin
> > >> > ( origin = origin - spacing/2). Now images are well registered,
> > >> >
> > >> > - but now, there is a problem at image boundaries. All voxels close to
> > >> > the boundary (less than spacing/2 in all directions) are set to zero.
> > >> > This is incorrect since the size of the low-resolution have been setup
> > >> > to be exactly a multiple of the high-resolution image size.
> > >> >
> > >> > Here a screenshot and some code I use.
> > >> >
> > >> > Thank you
> > >> >
> > >> > stan
> > >> >
> > >> >
> > >> >
> > >> >  typedef short      PixelType;
> > >> >  const   unsigned int        Dimension = 3;
> > >> >  typedef itk::Image< PixelType, Dimension >    ImageType;
> > >> >  typedef itk::ImageFileReader< ImageType >  ReaderType;
> > >> >  typedef itk::ImageFileWriter< ImageType >  WriterType;
> > >> >  ReaderType::Pointer reader = ReaderType::New();
> > >> >  ReaderType::Pointer reader_input = ReaderType::New();
> > >> >  WriterType::Pointer writer = WriterType::New();
> > >> >
> > >> >  //Reading reference image
> > >> >  reader->SetFileName( reference_file  );
> > >> >  reader->Update();
> > >> >  ImageType::Pointer referenceImage = reader->GetOutput();
> > >> >
> > >> >  //Reading input image
> > >> >  reader_input->SetFileName( input_file  );
> > >> >  reader_input->Update();
> > >> >  ImageType::Pointer inputImage = reader_input->GetOutput();
> > >> >
> > >> >  typedef itk::ResampleImageFilter<ImageType,ImageType> FilterType;
> > >> >  FilterType::Pointer filter = FilterType::New();
> > >> >
> > >> >  typedef itk::AffineTransform< double, Dimension >  TransformType;
> > >> >  TransformType::Pointer transform = TransformType::New();
> > >> >  transform -> SetIdentity();
> > >> >  filter->SetTransform( transform );
> > >> >
> > >> >  typedef itk::BSplineInterpolateImageFunction< ImageType, double, int
> > >> >  >  InterpolatorType;
> > >> >
> > >> >  InterpolatorType::Pointer interpolator = InterpolatorType::New();
> > >> >  interpolator->SetSplineOrder(interp);
> > >> >  filter->SetInterpolator( interpolator );
> > >> >
> > >> >  filter->SetDefaultPixelValue( 0 );
> > >> >
> > >> >  //Initialize with reference image information
> > >> >  filter->SetOutputSpacing( referenceImage->GetSpacing() );
> > >> >
> > >> >  ImageType::SpacingType spacing = inputImage->GetSpacing();
> > >> >  ImageType::PointType origin = inputImage->GetOrigin();
> > >> >  origin[0] -= spacing[0]/2;
> > >> >  origin[1] -= spacing[1]/2;
> > >> >  origin[2] -= spacing[2]/2;
> > >> >
> > >> >  filter->SetOutputOrigin( origin );
> > >> >
> > >> >  filter->SetSize( referenceImage->GetLargestPossibleRegion().GetSize() );
> > >> >
> > >> >  //Do the resampling
> > >> >  filter->SetInput( inputImage );
> > >> >  filter->Update();
> > >> >  ImageType::Pointer outputImage = filter->GetOutput();
> > >> >
> > >> >  //Saving the result
> > >> >  writer->SetFileName( output_file );
> > >> >  writer->SetInput( outputImage );
> > >> >  writer->Update();
> > >> >
> > >> >
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