[Insight-users] [Gdcm2] Bad rescale slope/intercept with gdcm 2.0.15 via itkGDCMImageIO
Roger Bramon Feixas
rogerbramon at gmail.com
Thu Jul 29 06:25:45 EDT 2010
Great! I successfully built it after applying the patch.
Thanks,
Roger
On Thu, Jul 29, 2010 at 10:37 AM, Mathieu Malaterre <
mathieu.malaterre at gmail.com> wrote:
> [top post]
>
> This has been fixed in ITK CVS HEAD/ git master:
>
>
> http://itk.org/gitweb?p=ITK.git;a=commitdiff;h=93833edb2294c0190af9e6c0de26e9485399a7d3
>
> Simply apply that to your ITK version XX
>
> HTH
>
> On Thu, Jul 29, 2010 at 10:29 AM, Roger Bramon Feixas
> <rogerbramon at gmail.com> wrote:
> > Hi,
> > I'm working with Jesús and we found the problem: we upgraded from GDCM
> > 2.0.14 to 2.0.15 but ITK 3.18 wasn't been rebuilt. However, we need to
> build
> > GDCM 2.0.15 with VTK support but then it isn't possible to build ITK
> using
> > external GDCM 2.0.15+VTK as we're discussing
> > here: http://www.itk.org/pipermail/insight-users/2010-July/037515.html.
> > Have you found a solution to be able to compile ITK?
> > Thanks!
> > Roger
> > On Tue, Jul 27, 2010 at 1:34 PM, Mathieu Malaterre
> > <mathieu.malaterre at gmail.com> wrote:
> >>
> >> You said you were using ITK+GDCM2. If this is the case then this is
> >> already integrated for you.
> >>
> >> BTW, this does not impact CT, so there is something else going on, on
> >> your setup.
> >>
> >> HTH
> >>
> >> On Tue, Jul 27, 2010 at 1:13 PM, Jesús Spínola <jspinola at gmail.com>
> >> wrote:
> >> > Hi Mathieu,
> >> > I get the same result as you running "gdcmviewer". The issue is
> >> > occurring
> >> > under windows, I haven't tested under any other operating system.
> >> > How can I achieve the "--force-rescale" behaviour with my sample
> >> > program?
> >> > I'll take a look to the gdcmviewer app too.
> >> >
> >> > On Fri, Jul 23, 2010 at 7:17 PM, Mathieu Malaterre
> >> > <mathieu.malaterre at gmail.com> wrote:
> >> >>
> >> >> Jesús,
> >> >>
> >> >> First thing first what do you get when you run:
> >> >>
> >> >> $ gdcmviewer --force-rescale -V 05119865-mr-siemens-avanto-syngo.dcm
> >> >>
> >> >> I am getting:
> >> >>
> >> >> ...
> >> >> Increments: (0, 0, 0)
> >> >> Extent: (0, 447, 0, 335, 0, 0)
> >> >>
> >> >> Range: -1186 526
> >> >>
> >> >> Which seems about right, according to your number.
> >> >>
> >> >> Thanks !
> >> >>
> >> >>
> >> >> On Fri, Jul 23, 2010 at 10:56 AM, Jesús Spínola <jspinola at gmail.com
> >
> >> >> wrote:
> >> >> > Hi,
> >> >> > So far I was using gdcm 2.0.14 and I was able to read any image
> with
> >> >> > no
> >> >> > problem, but I upgraded recently to gdcm 2.0.15 and I found a
> problem
> >> >> > reading some CT and MR DICOM image files.
> >> >> > The way I'm reading DICOM files is using itkGDCMImageIO with
> >> >> > itkImageSeriesReader and then filtering the output to vtk for the
> >> >> > image
> >> >> > rendering.
> >> >> > The problem is that some images are now (gdcm 2.0.15) loaded with a
> >> >> > different scalar range than before (gdcm 2.0.14), hence they are
> not
> >> >> > displayed properly with the default window/level setting (almost
> >> >> > completely
> >> >> > white in most CT cases for instance). I observed that the images
> with
> >> >> > trouble were those containing rescale intercept/slope tags with
> some
> >> >> > value.
> >> >> > The images with no rescale intercept/slope present are displayed as
> >> >> > expected, so my guess is there is some problem regarding the
> >> >> > intercept/slope
> >> >> > rescale computation.
> >> >> > I've written a little program which reads a DICOM image and renders
> >> >> > it
> >> >> > with
> >> >> > vtk to reproduce the bug. Then I compiled it against gdcm 2.0.14
> and
> >> >> > 2.0.15
> >> >> > to see the differences between each other. The source code is at
> the
> >> >> > end
> >> >> > of
> >> >> > this e-mail.
> >> >> > I've been testing with some DICOM images
> >> >> >
> >> >> > from
> http://www.creatis.insa-lyon.fr/~jpr/PUBLIC/gdcm/gdcmData.tar.gz.
> >> >> > Some
> >> >> > of these test images are valid to reproduce the problem, in this
> case
> >> >> > I'll
> >> >> > show you the results with
> >> >> > MR-MONO2-12-shoulder.dcm, CT-SIEMENS-Icone-With-PaletteColor.dcm
> >> >> > and 05119865-mr-siemens-avanto-syngo.dcm.
> >> >> > In the following table I show some of the relevant information of
> >> >> > each
> >> >> > image
> >> >> > and the scalar range I get building the program against gdcm 2.0.14
> >> >> > and
> >> >> > 2.0.15. The right scalar range is the one obtained with gdcm
> 2.0.14.
> >> >> > The
> >> >> > result is specially bad with the MR-MONO2-12-shoulder.dcm image.
> >> >> > File WW,WL Bits Allocated/Stored Rescale Slope/Intercept Scalar
> >> >> > Range:
> >> >> > 2.0.14 Build 2.0.15 Build
> >> >> > MR-MONO2-12-shoulder.dcm 2000,1000 16/12 3.774114, 0.000061 0..2245
> >> >> > -32065..32556
> >> >> > CT-SIEMENS-Icone-With-PaletteColor.dcm 350,40 16/12 1, -1024
> >> >> > -1024..981
> >> >> > 0..2005
> >> >> > 05119865-mr-siemens-avanto-syngo.dcm 1538,98 16/12 2, -4096
> >> >> > -1186..526
> >> >> > 1455..2311
> >> >> >
> >> >> > I tested with itk 3.18 and vtk 5.6, (the vtk version might not
> make
> >> >> > any
> >> >> > sense in the results because the problem is just in the reading
> >> >> > stage).
> >> >> > (Look at some screenshots of the results)
> >> >> > //
> >> >> > // SOURCE CODE
> >> >> > //
> >> >> > //
> >> >> > // You'll need also itkImageToVTKImageFilter class, available in
> the
> >> >> > InsightApplications package under "Auxiliary\vtk" folder
> >> >> > //
> >> >> > // Usage: main.exe DICOMFilename [WindowWidth WindowLevel]
> >> >> > #include <vtkImageviewer2.h>
> >> >> > #include <vtkRenderWindowInteractor.h>
> >> >> > #include <vtkRenderWindow.h>
> >> >> > #include <itkImage.h>
> >> >> > #include <itkImageSeriesReader.h>
> >> >> > #include <itkGDCMImageIO.h>
> >> >> > #include "itkImageToVTKImageFilter.h" //Converts an ITK image into
> a
> >> >> > VTK
> >> >> > image and plugs a itk data pipeline to a VTK datapipeline.
> >> >> > int main(int argc, char* argv[])
> >> >> > {
> >> >> > // Voxel type and image dimension
> >> >> > typedef signed short int VoxelType;
> >> >> > typedef VoxelType ItkPixelType;
> >> >> > static const unsigned int VDimension = 3;
> >> >> > // Itk Image type
> >> >> > typedef itk::Image<ItkPixelType, VDimension> ItkImageType;
> >> >> > typedef ItkImageType::Pointer ItkImageTypePointer;
> >> >> >
> >> >> > // Series reader
> >> >> > typedef itk::ImageSeriesReader<ItkImageType> SeriesReaderType;
> >> >> > typedef itk::GDCMImageIO ImageIOType;
> >> >> > // itk2vtk filter
> >> >> > typedef itk::ImageToVTKImageFilter<ItkImageType>
> >> >> > ItkToVtkFilterType;
> >> >> > /// DICOM Reader
> >> >> > SeriesReaderType::Pointer m_seriesReader =
> >> >> > SeriesReaderType::New();
> >> >> > ImageIOType::Pointer m_gdcmIO = ImageIOType::New();
> >> >> >
> >> >> > m_seriesReader->SetImageIO(m_gdcmIO);
> >> >> > ItkToVtkFilterType::Pointer m_itkToVtkFilter =
> >> >> > ItkToVtkFilterType::New();
> >> >> > // Check the number of parameters given
> >> >> > if (argc >= 2)
> >> >> > {
> >> >> > // Create the renderer object and configure it
> >> >> > vtkImageViewer2 *viewer = vtkImageViewer2::New();
> >> >> > vtkRenderWindowInteractor *interactor =
> >> >> > vtkRenderWindowInteractor::New();
> >> >> > viewer->SetupInteractor(interactor);
> >> >> > // Set the first argument as the input filename to read
> >> >> > // Atention: We don't check whether the file is valid or
> not
> >> >> > m_seriesReader->SetFileName(argv[1]);
> >> >> > m_itkToVtkFilter->SetInput(m_seriesReader->GetOutput());
> >> >> > try
> >> >> > {
> >> >> > m_itkToVtkFilter->Update();
> >> >> > }
> >> >> > catch (itk::ExceptionObject & exception)
> >> >> > {
> >> >> > std::cerr << "Exception caught!" <<
> >> >> > exception.GetDescription()
> >> >> > << std::endl;
> >> >> > }
> >> >> > // Show some information about the image
> >> >> > m_itkToVtkFilter->GetOutput()->Print(std::cout);
> >> >> > std::cerr << "** Scalar Range **" << std::endl;
> >> >> > std::cerr <<
> >> >> > m_itkToVtkFilter->GetOutput()->GetScalarRange()[0]
> >> >> > <<
> >> >> > ".." << m_itkToVtkFilter->GetOutput()->GetScalarRange()[1] <<
> >> >> > std::endl;
> >> >> > // Set the viewer input (DICOM File) and do the rendering
> >> >> > stuff
> >> >> > viewer->SetInput(m_itkToVtkFilter->GetOutput());
> >> >> >
> >> >> > // We can optionally set the window/level through the
> >> >> > arguments
> >> >> > if (argc >=4)
> >> >> > {
> >> >> > std::cout << "Applying given ww/wl: " << argv[2] << ",
> "
> >> >> > <<
> >> >> > argv[3] << std::endl;
> >> >> > viewer->SetColorWindow(atof(argv[2]));
> >> >> > viewer->SetColorLevel(atof(argv[3]));
> >> >> > }
> >> >> > else
> >> >> > {
> >> >> > std::cout << "Applying default ww/wl: 256, 128" <<
> >> >> > std::endl;
> >> >> > viewer->SetColorWindow(256);
> >> >> > viewer->SetColorLevel(128);
> >> >> > }
> >> >> >
> >> >> > viewer->Render();
> >> >> > interactor->Start();
> >> >> > }
> >> >> > else
> >> >> > {
> >> >> > std::cerr << "Usage: main.exe DICOMFilename [WindowWidth
> >> >> > WindowLevel]" << std::endl;
> >> >> > }
> >> >> > return 0;
> >> >> > }
> >> >> > --
> >> >> > Jesús Spínola
> >> >> >
> >> >> > _____________________________________
> >> >> > Powered by www.kitware.com
> >> >> >
> >> >> > Visit other Kitware open-source projects at
> >> >> > http://www.kitware.com/opensource/opensource.html
> >> >> >
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> >> >> >
> >> >> > Please keep messages on-topic and check the ITK FAQ at:
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> >> >> >
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> >> >> > http://www.itk.org/mailman/listinfo/insight-users
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Mathieu
> >> >
> >> >
> >> >
> >> > --
> >> > Jesús Spínola
> >> >
> >>
> >>
> >>
> >> --
> >> Mathieu
> >>
> >>
> >>
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> >
> >
>
>
>
> --
> Mathieu
>
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