[Insight-users] Boundary problem when resampling?

[Bill Lorensen]

With centered off, the sample value is considered to be at the pixel
corner. When it is on, the sample is at the pixel center.

In itk 3.16, we changed the defualt from off to on.

Bill

On Mon, Nov 16, 2009 at 5:28 AM, stan <stan.oubel at gmail.com> wrote:
> 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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