[ITK] [ITK-users] Writing a DICOM file while preserving input image properties
Sarthak P
scapegoat.sarthak at gmail.com
Thu Mar 9 10:25:09 EST 2017
Hi Matt,
Yes I do know that. I have tried to put the spacing information from the
itk::Image using various combinations with the tags 0018|0088 (slice
thickness) and 0018|0050 (spacing between slices) but to no avail.
Thanks for your help,
Sarthak
On Thu, Mar 9, 2017 at 9:47 AM, Matt McCormick <matt.mccormick at kitware.com>
wrote:
> HI Sarthak,
>
> The slice thickness is different from the spacing between slices. In
> DICOM, slice thickness is related to the point spread function of the
> imaging system and slice spacing is related to digital sampling.
>
> Hope this helps,
> Matt
>
> On Thu, Mar 9, 2017 at 9:30 AM, Sarthak P <scapegoat.sarthak at gmail.com>
> wrote:
> > Hi Matt,
> >
> > Thanks for the response.
> >
> > I don't think I am having issues with writing into the tags since I am
> able
> > to read the correct information I am writing (for instance, the tag
> > "0020|0032" is always populated with the physical coordinate of the
> specific
> > slice in a correct manner both during writing and reading). In an
> example,
> > the slice thickness should be "2" and the separation between the dicom
> > slices is "2", which is correct. But when ITK is reading this
> collection, it
> > keeps the slice thickness at "1". I am seeing the same behavior in other
> > applications as well (ITK-SNAP, etc.).
> >
> > Could there be some tag I am missing to write? Since my last post, I
> tried
> > writing only to the tag "0020|0032"; the output dictionary array gets
> > populated properly but the file is still not written as expected. I am
> using
> > ITK 4.11, BTW.
> >
> > Best,
> > Sarthak
> >
> > On Thu, Mar 9, 2017 at 9:20 AM, Matt McCormick <
> matt.mccormick at kitware.com>
> > wrote:
> >>
> >> Hi Sarthak,
> >>
> >> DICOM export requires improved typing to produce a valid set of tags.
> >> This work has been started here:
> >>
> >> https://github.com/KitwareMedical/ITKDICOM
> >>
> >> but the implementation is in initial stages. I would be happy to
> >> provide guidance if you would like to move it forward.
> >>
> >> Thanks,
> >> Matt
> >>
> >> On Wed, Mar 8, 2017 at 3:11 PM, Sarthak P <scapegoat.sarthak at gmail.com>
> >> wrote:
> >> > Hello All,
> >> >
> >> > I am trying to write a DICOM image but I want to preserve the
> properties
> >> > from the input image (origin, direction, spacing, etc.). The ITK
> >> > examples do
> >> > not show how to do this properly and anything I have done with the
> dicom
> >> > tags hasn't worked. Any help would be much appreciated.
> >> >
> >> > Here is what I have so far:
> >> >
> >> > //////////
> >> > const std::string dataDir = argv[1];
> >> > const std::string inputFile = dataDir + "/inputImage.nii.gz";
> >> > const std::string outputDir = dataDir + "/test/";
> >> >
> >> > using ImageTypeToRead = itk::Image< float, 3 >;
> >> > using ImageTypeToWrite = itk::Image< short, 3 >;
> >> > auto inputImage = cbica::ReadImageWithOrientFix< itk::Image< float,
> 3
> >> > >
> >> >>(inputFile);
> >> > auto imageToWrite = inputImage;
> >> >
> >> > auto dicomIO = itk::GDCMImageIO::New();
> >> >
> >> > auto seriesWriter = itk::ImageSeriesWriter< ImageTypeToWrite,
> >> > itk::Image<ImageTypeToWrite::PixelType, 2> >::New();
> >> >
> >> > auto namesGenerator = itk::NumericSeriesFileNames::New();
> >> > auto start = imageToWrite->GetLargestPossibleRegion().GetIndex();
> >> > auto size = imageToWrite->GetLargestPossibleRegion().GetSize();
> >> > namesGenerator->SetSeriesFormat((outputDir +
> >> > "/image%03d.dcm").c_str());
> >> > namesGenerator->SetStartIndex(start[2]);
> >> > namesGenerator->SetEndIndex(start[2] + size[2] - 1);
> >> > namesGenerator->SetIncrementIndex(1);
> >> >
> >> > auto castFilter = itk::CastImageFilter<ImageTypeToRead,
> >> > ImageTypeToWrite>::New();
> >> > castFilter->SetInput(imageToWrite);
> >> > castFilter->Update();
> >> >
> >> > seriesWriter->SetInput(castFilter->GetOutput());
> >> > seriesWriter->SetImageIO(dicomIO);
> >> > seriesWriter->SetFileNames(namesGenerator->GetFileNames());
> >> >
> >> > typename itk::ImageSeriesReader< ImageTypeToRead
> >> > >::DictionaryArrayType
> >> > outputArray;
> >> >
> >> > // this doesn't work at all - was kind of hoping it would do the
> heavy
> >> > lifting for me
> >> > //dicomIO->SetOrigin(0, imageToWrite->GetOrigin()[0]);
> >> > //dicomIO->SetOrigin(1, imageToWrite->GetOrigin()[1]);
> >> > //dicomIO->SetOrigin(2, imageToWrite->GetOrigin()[2]);
> >> > //dicomIO->SetSpacing(0, imageToWrite->GetSpacing()[0]);
> >> > //dicomIO->SetSpacing(1, imageToWrite->GetSpacing()[1]);
> >> > //dicomIO->SetSpacing(2, imageToWrite->GetSpacing()[2]);
> >> > //dicomIO->SetDimensions(0,
> >> > imageToWrite->GetLargestPossibleRegion().GetSize()[0]);
> >> > //dicomIO->SetDimensions(1,
> >> > imageToWrite->GetLargestPossibleRegion().GetSize()[1]);
> >> > //dicomIO->SetDimensions(2,
> >> > imageToWrite->GetLargestPossibleRegion().GetSize()[2]);
> >> > // this doesn't work at all
> >> >
> >> > for (size_t i = 0; i <
> >> > imageToWrite->GetLargestPossibleRegion().GetSize()[2]; i++)
> >> > {
> >> > auto dict = new itk::ImageSeriesReader< ImageTypeToRead
> >> >>::DictionaryType;
> >> > typename ImageTypeToWrite::PointType position;
> >> > typename ImageTypeToWrite::IndexType index;
> >> > index[0] = 0;
> >> > index[1] = 0;
> >> > index[2] = i;
> >> > imageToWrite->TransformIndexToPhysicalPoint(index, position);
> >> > // tags extracted from dicom lookup
> >> > http://dicomlookup.com/lookup.asp
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0020|0032",
> >> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) +
> "\\"
> >> > +
> >> > std::to_string(position[2])); // patient position
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0018|5100",
> >> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) +
> "\\"
> >> > +
> >> > std::to_string(position[2]));
> >> > itk::EncapsulateMetaData<std::string>(*dict, "2020|0010",
> >> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) +
> "\\"
> >> > +
> >> > std::to_string(position[2]));
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0018|5101",
> >> > std::to_string(position[0]) + "\\" + std::to_string(position[1]) +
> "\\"
> >> > +
> >> > std::to_string(position[2]));
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0018|0050",
> >> > std::to_string(imageToWrite->GetSpacing()[2])); // Slice Thickness
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0018|0088",
> >> > std::to_string(imageToWrite->GetSpacing()[2])); // Spacing Between
> >> > Slices
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0008|0008",
> >> > "DERIVED\\SECONDARY"); // Image Type
> >> > itk::EncapsulateMetaData<std::string>(*dict, "0008|0064", "DV");
> //
> >> > Conversion Type
> >> >
> >> > outputArray.push_back(dict);
> >> > }
> >> >
> >> > seriesWriter->SetMetaDataDictionaryArray(&outputArray); // no
> >> > dictionary
> >> > information present without seriesReader
> >> >
> >> > try
> >> > {
> >> > seriesWriter->Write();
> >> > }
> >> > catch (itk::ExceptionObject &e)
> >> > {
> >> > std::cerr << "Error occurred while trying to write the image '" <<
> >> > outputDir << "': " << e.what() << "\n";
> >> > exit(EXIT_FAILURE);
> >> > }
> >> >
> >> > //////////
> >> >
> >> > Thanks a ton,
> >> > Sarthak
> >> >
> >> > _____________________________________
> >> > Powered by www.kitware.com
> >> >
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> >> >
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> >> >
> >> > Please keep messages on-topic and check the ITK FAQ at:
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> >> >
> >
> >
>
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