[ITK-users] Resampling and manual image

[Matt McCormick]

Hi Guillaume,

A few pointers may help:

- Make sure to use ITK 4.5.2 or later, which has fixes for writing DICOM
series spacing.
- Use a different format than DICOM when possible for writing out generated
files.  It is difficult to get the tags correct, especially with an
operation like resampling where the number of slices can change.
- See this guide for further tips [1].
- See this example for reference [2].

Hope this helps,
Matt

[1] http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM

[2] http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM


On Tue, Apr 22, 2014 at 2:43 PM, Guillaume Lemaître
<g.lemaitre58 at gmail.com>wrote:

> 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 Guillaume PhD CandiateMSc Erasmus Mundus ViBOT
> (Vision-roBOTic)MSc Business Innovation and Technology Management (in
> progress) *
> g.lemaitre58 at gmail.com
>
> *ViCOROB - Computer Vision and Robotic Team*
> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona
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>
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