[Insight-users] GDCM crashes when reading some dicom images

[Jesús Spí­nola]

On Fri, Apr 25, 2008 at 12:26 PM, Mathieu Malaterre <
mathieu.malaterre at gmail.com> wrote:

> On a different subject what anonymizer did you use ? It could not cope
> with a bunch of public elements, and inserted a VR=UN when doing the
> conversion from Implicit encoding to Explicit encoding.
>

With a Phillips workstation. I don't remember the exact application it was,
but I guess it's the EasyVision application.


> -Mathieu
>
> On Thu, Apr 24, 2008 at 10:10 PM, Jesús Spí­nola <jspinola at gmail.com>
> wrote:
> > Hello,
> >
> > I'm using itk 2.8.1 and I have a problem reading some DICOM images with
> > itkGDCMImageIO. For most of images I opened since now, it works ok, but
> I
> > have images from several studies that is not able to open because it
> crashes
> > with a SIGFPE (floating point exception). When debugging, this is the
> > message after crashing
> >
> > Program received signal SIGFPE, Arithmetic exception.
> > [Switching to Thread -1223084336 (LWP 6551)]
> >  0xb7de14e6 in gdcm::PixelReadConvert::ConvertReArrangeBits () from
> > /usr/lib/InsightToolkit/libitkgdcm.so.2.8
> >
> >
> > and the backtrace is the following:
> >
> >
> >  #0  0xb7de14e6 in gdcm::PixelReadConvert::ConvertReArrangeBits () from
> > /usr/lib/InsightToolkit/libitkgdcm.so.2.8
> > #1  0xb7de9c31 in gdcm::PixelReadConvert::ReadAndDecompressPixelData ()
> from
> > /usr/lib/InsightToolkit/libitkgdcm.so.2.8
> >  #2  0xb7dbd69c in gdcm::FileHelper::GetRaw () from
> > /usr/lib/InsightToolkit/libitkgdcm.so.2.8
> > #3  0xb7dbebf2 in gdcm::FileHelper::GetImageData () from
> > /usr/lib/InsightToolkit/libitkgdcm.so.2.8
> >  #4  0xb7ee1892 in itk::GDCMImageIO::Read () from
> > /usr/lib/InsightToolkit/libITKIO.so.2.8
> > #5  0x08061964 in itk::ImageFileReader<itk::Image<int, 3u>,
> > itk::DefaultConvertPixelTraits<int> >::GenerateData ()
> >  #6  0xb7a62380 in itk::ProcessObject::UpdateOutputData () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> > #7  0xb7a1f969 in itk::DataObject::UpdateOutputData () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> >  #8  0xb7a1f770 in itk::DataObject::Update () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> > #9  0xb7a5ffca in itk::ProcessObject::UpdateLargestPossibleRegion ()
> from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> >  #10 0x0805d6c0 in itk::ImageSeriesReader<itk::Image<int, 3u>
> > >::GenerateData ()
> > #11 0xb7a62380 in itk::ProcessObject::UpdateOutputData () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> >  #12 0xb7a1f969 in itk::DataObject::UpdateOutputData () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> > #13 0xb7a1f770 in itk::DataObject::Update () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> >  #14 0xb7a60062 in itk::ProcessObject::Update () from
> > /usr/lib/InsightToolkit/libITKCommon.so.2.8
> > #15 0x0804e0f4 in main ()
> >
> > To test this problem I've writen a little program I've attached
> > (gdcmBug.cpp) reproducing the problem. You can use the following
> anonymized
> > study ( http://hades.udg.edu/~chus/study1.tar.gz<http://hades.udg.edu/%7Echus/study1.tar.gz>) with some series to test
> > this bug. It crashes with any of the images of the study.
> >
> > I also tried to read the same images with other libraries such as vtk or
> > dcmtk and they're able to open the same images successfully.
> >
> > Assuming ITKINCLUDEDIR is /usr/include/InsightToolkit and ITKLIBDIR is
> > /usr/lib/InsightToolkit, the compile command for g++ is the following
> >
> >  g++ -o gdcmBug gdcmBug.o -I. -I/usr/include/InsightToolkit
> > -I/usr/include/InsightToolkit/IO -I/usr/include/InsightToolkit/gdcm/src
> > -L/usr/lib/InsightToolkit -lITKIO -litkgdcm
> >
> > To run this test you have to pass by argument the files you want to
> read.
> >
> > For example, if you want to read 3 images (im1, im2, im3) from the same
> > series:
> >
> > $>gdcmBug im1 im2 im3
> >
> > If you want to test with only one single image
> >
> > $>gdcmbug im1
> >
> > and so on...
> >
> > I tested this under Linux Mandriva 2008.0 and Kubuntu Feisty 7.04.
> >
> > Maybe this bug is resolved in a more recent version of itk, but I don't
> know
> > it. If so, let me know which version has solved this problem.
> >
> > I hope this test and the images I provided can help to find the problem.
> I
> > have more images to reproduce the problem, if necessary.
> >
> >
> > Thanks in advance!
> >
> > _______________________________________________
> >  Insight-users mailing list
> >  Insight-users at itk.org
> >  http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>
>
>
> --
> Mathieu
>
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