[Insight-users] [Gdcm2] Bad rescale slope/intercept with gdcm 2.0.15 via itkGDCMImageIO

Mathieu Malaterre mathieu.malaterre at gmail.com
Thu Jul 29 04:37:18 EDT 2010


[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
>> >> >
>> >> > _____________________________________
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>> >> >
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>> >> >
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>> >> >
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>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Mathieu
>> >
>> >
>> >
>> > --
>> > Jesús Spínola
>> >
>>
>>
>>
>> --
>> Mathieu
>>
>>
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>
>



-- 
Mathieu


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