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

[Mathieu Malaterre]

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.

-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 ) 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!
>
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>
>



-- 
Mathieu