[ITK] Invalid read in itkImageIOBase.cxx:167 when setting ImageIO on itkSeriesWriter

[Matt McCormick]

Hi Coert,

I am having a hard time following -- which file/line numbers are is
the input image in the ImageIO object?

Thanks,
Matt

On Fri, Apr 11, 2014 at 4:01 PM, Coert Metz <c.metz at quantib.com> wrote:
> Dear Matt,
>
> Thanks for your reply. I see that the fix consists of changing the loop
> condition at line 166 of itkImageIOBase.cxx. The thing I still do not
> understand is why the itkImageSeriesWriter is setting the input image in the
> ImageIO object. It seems to me that the actual problem lies there, but I
> might be wrong. Can you explain this?
>
> Kind regards,
> Coert Metz
>
>
> On Fri, Apr 11, 2014 at 5:33 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Coert,
>>
>> Thank you for you detailed description of the issue and discussing it
>> with the community.
>>
>> This bug has been around for quite some time, but it was discovered
>> and fixed [1] recently when improving test coverage.
>>
>> The fix is available in the v4.5.2 release.
>>
>> Thanks,
>> Matt
>>
>> [1]
>> http://itk.org/gitweb?p=ITK.git;a=commit;h=895c6fb83f0670e8464d11a023043639f399ea55
>>
>> On Fri, Apr 11, 2014 at 11:21 AM, Coert Metz <c.metz at quantib.com> wrote:
>> > Dear ITK developers,
>> >
>> > We think we have spotted a bug in the itkImageSeriesWriter which is
>> > causing
>> > a valgrind warning. The valgrind warning is the following:
>> >
>> > ====================
>> > 0xB3D961: itk::ImageIOBase::SetDirection(unsigned int,
>> > vnl_vector<double>
>> > const&) (itkImageIOBase.cxx:167)
>> > 0x680501: itk::ImageFileWriter<itk::Image<short, 2u> >::Write()
>> > (itkImageFileWriter.hxx:223)
>> > 0x67739A: itk::ImageFileWriter<itk::Image<short, 2u> >::Update()
>> > (itkImageFileWriter.h:166)
>> > 0x684673: itk::ImageSeriesWriter<itk::Image<float, 3u>,
>> > itk::Image<short,
>> > 2u> >::WriteFiles() (itkImageSeriesWriter.hxx:372)
>> > 0x684A44: itk::ImageSeriesWriter<itk::Image<float, 3u>,
>> > itk::Image<short,
>> > 2u> >::GenerateData() (itkImageSeriesWriter.hxx:178)
>> > 0x68A1D2: itk::ImageSeriesWriter<itk::Image<float, 3u>,
>> > itk::Image<short,
>> > 2u> >::Write() (itkImageSeriesWriter.hxx:105)
>> > 0x677178: itk::ImageSeriesWriter<itk::Image<float, 3u>,
>> > itk::Image<short,
>> > 2u> >::Update() (itkImageSeriesWriter.h:138)
>> > ====================
>> >
>> > We are using ITK 4.5.
>> >
>> > The code we use basically boils down to:
>> >
>> > ====================
>> > // Create GDCM Image IO object.
>> > typedef itk::GDCMImageIO ImageIOType;
>> > ImageIOType::Pointer gdcm_io = ImageIOType::New();
>> >
>> > // Set Image Type tag.
>> > itk::MetaDataDictionary& dictionary = gdcm_io->GetMetaDataDictionary();
>> > std::string tagkey, value;
>> > tagkey = "0008|0008";  // Image Type
>> > value = "DERIVED\\SECONDARY";
>> > itk::EncapsulateMetaData<std::string>(dictionary, tagkey, value);
>> >
>> > // Write DICOM series.
>> > typename SeriesWriterType::Pointer writer = SeriesWriterType::New();
>> > writer->SetInput(quantib_to_itk);
>> > writer->SetImageIO(gdcm_io);
>> > writer->SetFileNames(...filenames...);
>> > writer->Update();
>> > ====================
>> >
>> > We have tracked down the issue to the following:
>> >
>> > As set the ImageIO object explicitly, the code at line 354 of
>> > itkImageSeriesWriter.hxx is executed:
>> >
>> > ====================
>> > EncapsulateMetaData<  unsigned int   >(dictionary,
>> > ITK_NumberOfDimensions,
>> > inputImageDimension);
>> > ====================
>> >
>> > This explicitly sets the number of image dimensions of the dictionary
>> > input
>> > image in the ImageIO instance. In this case we have a 3D image and write
>> > 2D
>> > slices, so 3 will be set in the ImageIO instance dictionary and passed
>> > to
>> > the itkImageFileWriter when writing the 2D slices. The
>> > itkImageFileWriter
>> > reads the ITK_NumberOfDimensions tag from the dictionary to set the size
>> > of,
>> > among others, the direction matrix (line 704 of itkGDCMImageIO.cxx).
>> > This
>> > will in the end result in reading an invalid memory location in
>> > itkImageIOBase at line 167, which loops over 3 dimensions while it
>> > should
>> > loop over 2 dimensions. The code at line 356-368 also seems strange to
>> > me,
>> > as the direction matrix should be 2x2, I think.
>> >
>> > Maybe we are overlooking something, so I am curious if this is a real
>> > bug,
>> > or that we maybe use the writer and the ImageIO object in the wrong way.
>> > Curious for your insights.
>> > --
>> > Coert Metz, PhD
>> > Research & Development Engineer  |  Quantib B.V.
>> > c.metz at quantib.com  |  +31 650 68 60 28
>> >
>> > This message may contain confidential or privileged information. If you
>> > are
>> > not the addressee, please return the message to its sender and delete it
>> > from your files.
>> > _______________________________________________
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>> >
>
>
>
>
> --
> Coert Metz, PhD
> Research & Development Engineer  |  Quantib B.V.
> c.metz at quantib.com  |  +31 650 68 60 28
>
> This message may contain confidential or privileged information. If you are
> not the addressee, please return the message to its sender and delete it
> from your files.