[Insight-users] translating image volume using affine transformation
michiel mentink
michael.mentink at st-hughs.ox.ac.uk
Mon Nov 30 04:53:54 EST 2009
might this be the same problem as in
problem with orientation of dicom output from segmentationwhere the dicom 3d
volume is changed in orientation?
Kind regards, Michael
On Mon, Nov 30, 2009 at 9:42 AM, michiel mentink <
michael.mentink at st-hughs.ox.ac.uk> wrote:
> Dear Bill,
>
> I indeed didn't define the origin correctly. However, now there seems to be
> a more
> serious problem.
>
> Since I'm not sure I can upload screenshots to this mailing list, I have
> put a
> ITKsnap screenshot of the original dcm volume view, together with output
> after
> the affine filter and code on this site:
>
> http://sites.google.com/site/michielmentink/programming/itk/image-translate
>
> You can see there that before and after the affine filter, using identity
> transformation,
> the filesize, number of pixels, and pixel sizes are identical.
>
> There is a small bit of the original volume visible in the resulting dicom
> volume, but
> it contains only image data on a eight slices and the slices are deformed.
>
> What I can make of the data, it seems that the filter has rotated the dicom
> volume
> so that the 'coronal' (seeing)from the front) view now shows the 'axial'
> view (seeing
> from above).
> Also, the image is flipped in both X and Y axis.
>
> If I change the Z origin to -69 instead of 69, most image slices actually
> contain the
> image data, but still the views have been changed completely, like
> mentioned before.
>
>
> What is going on?
> What I really want to do is load in a dicom volume, translate it in the X,
> Y, Z direction
> and save it. Normally, the affine filter should be used for this, right?
>
> For completeness, I've pasted the code again.
>
> Kind regards, Michael
>
>
>
>
>
> On Fri, Nov 27, 2009 at 4:05 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:
>
>> What is the origin, spacing and direction of the input volume?
>>
>> On Fri, Nov 27, 2009 at 9:59 AM, michiel mentink
>> <michael.mentink at st-hughs.ox.ac.uk> wrote:
>> > Dear all,
>> >
>> > I'm trying to make a simple function that translates a dicom volume by a
>> > certain amount.
>> > It first opens all dicom slides of an mri scan.
>> >
>> > To do this, I pasted DicomSeriesReadImageWrite2.cxx and
>> > ResampleImageFilter.cxx and adjusted
>> > the latter so it accepts 3 dimensions instead of two and uses integer
>> > instead of unsigned char.
>> >
>> > The function compiles and a .vtk volume is written. However, there's no
>> > image data in the file.
>> > It does display all pixels with value 100, as I set by:
>> > filter->SetDefaultPixelValue( 100 );
>> >
>> > questions:
>> > 1) am I too naive to think that the ResampleImageFilter can easily be
>> > extended from 2 to 3 dimensions?
>> > 2) if not, what did I do wrong?
>> >
>>
>
>
> #if defined(_MSC_VER)
> #pragma warning ( disable : 4786 )
> #endif
>
> #ifdef __BORLANDC__
> #define ITK_LEAN_AND_MEAN
> #endif
>
> #include "itkOrientedImage.h"
> #include "itkGDCMImageIO.h"
> #include "itkGDCMSeriesFileNames.h"
> #include "itkImageSeriesReader.h"
> #include "itkImageFileWriter.h"
> #include "itkResampleImageFilter.h"
>
> #include "itkAffineTransform.h"
> #include "itkNearestNeighborInterpolateImageFunction.h"
> // Software Guide : EndCodeSnippet
>
> int main( int argc, char* argv[] )
> {
>
> if( argc < 3 )
> {
> std::cerr << "Usage: " << std::endl;
> std::cerr << argv[0] << " DicomDirectory outputFileName [seriesName]"
>
> << std::endl;
> return EXIT_FAILURE;
> }
>
> typedef signed short PixelType;
> const unsigned int Dimension = 3;
>
> typedef itk::OrientedImage< PixelType, Dimension > ImageType;
>
> typedef itk::ImageSeriesReader< ImageType > ReaderType;
> ReaderType::Pointer reader = ReaderType::New();
>
> typedef itk::GDCMImageIO ImageIOType;
> ImageIOType::Pointer dicomIO = ImageIOType::New();
>
> reader->SetImageIO( dicomIO );
>
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>
> nameGenerator->SetUseSeriesDetails( true );
> nameGenerator->AddSeriesRestriction("0008|0021" );
>
> nameGenerator->SetDirectory( argv[1] );
>
> try
> {
> std::cout << std::endl << "The directory: " << std::endl;
> std::cout << std::endl << argv[1] << std::endl << std::endl;
> std::cout << "Contains the following DICOM Series: ";
> std::cout << std::endl << std::endl;
>
> typedef std::vector< std::string > SeriesIdContainer;
>
> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
>
> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
> while( seriesItr != seriesEnd )
> {
> std::cout << seriesItr->c_str() << std::endl;
> seriesItr++;
> }
>
> std::string seriesIdentifier;
>
> if( argc > 3 ) // If no optional series identifier
> {
> seriesIdentifier = argv[3];
> }
> else
> {
> seriesIdentifier = seriesUID.begin()->c_str();
> }
>
> std::cout << std::endl << std::endl;
> std::cout << "Now reading series: " << std::endl << std::endl;
> std::cout << seriesIdentifier << std::endl;
> std::cout << std::endl << std::endl;
>
> typedef std::vector< std::string > FileNamesContainer;
> FileNamesContainer fileNames;
>
> fileNames = nameGenerator->GetFileNames( seriesIdentifier );
> reader->SetFileNames( fileNames );
> try
> {
> reader->Update();
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex << std::endl;
> return EXIT_FAILURE;
> }
> }
> catch (itk::ExceptionObject &ex)
> {
> std::cout << ex << std::endl;
> return EXIT_FAILURE;
> }
> // return EXIT_SUCCESS;
>
>
> //////////////////////////////////////////////////////////////////////////////////////
> // FROM HERE NEW CODE
>
>
> /////////////////////////////////////////////////////////////////////////////////////
>
> // const unsigned int Dimension = 3;
> // typedef unsigned char InputPixelType;
> // typedef unsigned char OutputPixelType;
> typedef itk::Image< PixelType, Dimension > InputImageType;
> typedef itk::Image< PixelType, Dimension > OutputImageType;
> typedef itk::ImageFileWriter< ImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
>
> writer->SetFileName( argv[2] );
>
> typedef itk::ResampleImageFilter<ImageType,ImageType> FilterType;
> FilterType::Pointer filter = FilterType::New();
>
> typedef itk::AffineTransform< double, Dimension > TransformType;
> TransformType::Pointer transform = TransformType::New();
> filter->SetTransform( transform );
>
>
> typedef itk::NearestNeighborInterpolateImageFunction<ImageType, double >
> InterpolatorType;
> InterpolatorType::Pointer interpolator = InterpolatorType::New();
> filter->SetInterpolator( interpolator );
>
> filter->SetDefaultPixelValue( 100 ); // if pixel in output image not
> defined, what value?
>
> double spacing[ Dimension ];
> spacing[0] = 0.29; // pixel spacing in millimeters along X
> spacing[1] = 0.29; // pixel spacing in millimeters along Y
> spacing[2] = 3.3; // pixel spacing in millimeters along Z
>
>
> filter->SetOutputSpacing( spacing );
>
> double origin[ Dimension ];
> origin[0] = -174.22; // X space coordinate of origin
> origin[1] = -125.00; // Y space coordinate of origin
> origin[2] = 69.37; // Z space coordinate of origin
>
>
> filter->SetOutputOrigin( origin );
> ImageType::DirectionType direction;
> direction.SetIdentity();
> filter->SetOutputDirection( direction );
> ImageType::SizeType size;
>
> size[0] = 560; // number of pixels along X
> size[1] = 560; // number of pixels along Y
> size[2] = 26;
>
>
> filter->SetSize( size );
> filter->SetInput( reader->GetOutput() );
>
> writer->SetInput( filter->GetOutput() );
> writer->Update();
>
> std::cout << "Writing the image" << std::endl << std::endl;
>
>
> /* (this code not executed)
>
> TransformType::OutputVectorType translation;
> translation[0] = 0; // X translation in millimeters
> translation[1] = 0; // Y translation in millimeters
> translation[2] = 0; // Z translation in millimeters
>
>
> transform->Translate( translation );
> // Software Guide : EndCodeSnippet
>
> writer->SetInput( filter->GetOutput() );
>
> std::cout << "Writing the image as " << std::endl << std::endl;
> std::cout << argv[2] << std::endl << std::endl;
> writer->Update();
> */
>
> }
>
>
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