[ITK-users] Resampling and manual image

[Guillaume Lemaître]

Hi all,

I would like to have some advise to do the following task.

I have a set of annotated DICOM (binary 0 - 255 intensity) with a given
spacing, orientation and position. This manual segmentation is
corresponding to a prostate from an initial T2W sequence.

A part of DICOM, I have an MRSI sequence from Siemens (*.rda) in which the
header is containing information such as position, orientation and spacing
of the csi grid matrix used during the acquisition.

My aim would be to resample the annotated DICOM serie into a new DICOM
serie using the MRSI header. I attached the code that I tried to implement
to do this task but I don't succeed to obtain a correct serie when saving
into a DICOM serie. When opening the stored DICOM serie, it seems that the
field regarding the z spacing and the position of the first voxel are not
equal to the one of the rda manually affected during the resampling.

I was wondering to know the best way to do such manipulation. For instance,
it could be better to create a manual image using the field of the rda file
and just use the intensities

ResampleFilterType::Pointer resampler = ResampleFilterType::New();

    resampler->SetInput(inputAnnotatedVolume->GetOutput());

    resampler->SetTransform(transform);

    resampler->SetInterpolator(interpolator);

    // Create a type compatible to ITK

    // Define the new origin

    double* outputOrigin = new double [rdaPatient.getPositionPatient().size()];

    for(int i = 0; i < rdaPatient.getPositionPatient().size(); i++)

        outputOrigin[i] = rdaPatient.getPositionPatient()[i];

    resampler->SetOutputOrigin(outputOrigin);

    // Define the new spacing

    double* outputSpacing = new double [rdaPatient.getPixelSpacing().size()];

    for(int i = 0; i < rdaPatient.getPixelSpacing().size(); i++)

        outputSpacing[i] = rdaPatient.getPixelSpacing()[i];

    resampler->SetOutputSpacing(outputSpacing);

    // Define the new orientation

    typename ResampleFilterType::DirectionType outputDirection;

    //double ** outputDirection = new double* [3];

    //for(int i = 0; i < 3 ; i++)

    //    outputDirection[i] = new double [3];

    // Affect the new values

    outputDirection[0][0] = rdaPatient.getOrientationPatient()[0][0];

    outputDirection[0][1] = rdaPatient.getOrientationPatient()[0][1];

    outputDirection[0][2] = rdaPatient.getVoiNormalVector()[0];

    outputDirection[1][0] = rdaPatient.getOrientationPatient()[1][0];

    outputDirection[1][1] = rdaPatient.getOrientationPatient()[1][1];

    outputDirection[1][2] = rdaPatient.getVoiNormalVector()[1];

    outputDirection[2][0] = rdaPatient.getOrientationPatient()[2][0];

    outputDirection[2][1] = rdaPatient.getOrientationPatient()[2][1];

    outputDirection[2][2] = rdaPatient.getVoiNormalVector()[2];

    resampler->SetOutputDirection(inputAnnotatedVolume->GetOutput()->GetDirection());

    // Define the size of the ouput

    // Let's comput the new size

    InputImageType::SizeType outputSize;

    typedef InputImageType::SizeType::SizeValueType SizeValueType;

    outputSize[0] =
static_cast<SizeValueType>(rdaPatient.getCsiMatrixSize()[0]);

    outputSize[1] =
static_cast<SizeValueType>(rdaPatient.getCsiMatrixSize()[1]);

    outputSize[2] =
static_cast<SizeValueType>(rdaPatient.getCsiMatrixSize()[2]);

    resampler->SetSize(outputSize);

    // Resampling now

    resampler->Update();


Thanks in advance for the advices,

-- 




*LEMAÎTRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc
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g.lemaitre58 at gmail.com

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