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

[Matt McCormick]

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
>
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