[Insight-users] problem with orientation of dicom output from segmentation
John Drozd
john.drozd at gmail.com
Mon Nov 30 14:56:13 EST 2009
Hi Bill,
I installed the nightly build of 3D Slicer which includes Itk 3.16.
As you suggested I tried to compile my code with Itk 3.16, to see if the
"upside down" problem prevailed, but a new bigger problem exists for me with
using Itk 3.16.
I am perplexed that using Itk 3.16, my code segmenation faults when I invoke
reader->Update(),
for a dicom series or a dicom volume, whereas previously with itk 3.14 it
worked just fine.
I am currently trying to figure out how to set the "-g" compiler option for
the CMakeLists.txt file so I can run the gdb debugger on it to find out
where it segmentation faults.
I tried the command:
set (CMAKE_CXX_FLAGS_DEBUG_INIT "-g")
but so far that has not worked.
john
On Fri, Nov 27, 2009 at 4:48 PM, Bill Lorensen <bill.lorensen at gmail.com>wrote:
> John,
>
> Actually, Mathieu reported in response that updating to 3.16 may help.
> Can you try this first?
>
> Bill
>
> On Fri, Nov 27, 2009 at 12:42 PM, John Drozd <john.drozd at gmail.com> wrote:
> > Hi again,
> >
> > I was at home and I just figured out how to provide you this link to my
> data
> > remotely,
> > so I provide it now instead of on the weekend:
> >
> > Here is a link to my data (3D dicom volume):
> >
> > input volume for my ConnectedThresholdFilter code:
> > http://www.apmaths.uwo.ca/~jdrozd/correctedsubject5.dcm<http://www.apmaths.uwo.ca/%7Ejdrozd/correctedsubject5.dcm>
> >
> > output volume from my ConnectedThresholdFilter code:
> > http://www.apmaths.uwo.ca/~jdrozd/outsubject5.dcm<http://www.apmaths.uwo.ca/%7Ejdrozd/outsubject5.dcm>
> >
> > If you need my CMakeLists.txt file, just let me know.
> >
> > to run the code type:
> > ./ConnectedThresholdImageFilter correctedsubject5.dcm outsubject5.dcm 103
> > 142 95 17100 17300
> > and here is my code below:
> >
> >
> >
> > Below is my uncommented code:
> > /*
> > to run type:
> > ./ConnectedThresholdImageFilter correctedsubject5.dcm outsubject5.dcm 103
> > 142 95 17100 17300
> > */
> > #if defined(_MSC_VER)
> > #pragma warning ( disable : 4786 )
> > #endif
> > #ifdef __BORLANDC__
> > #define ITK_LEAN_AND_MEAN
> > #endif
> > #include "itkConnectedThresholdImageFilter.h"
> > #include "itkImage.h"
> > #include "itkCastImageFilter.h"
> > #include "itkCurvatureFlowImageFilter.h"
> > #include "itkImageFileReader.h"
> > #include "itkImageFileWriter.h"
> > #include "itkGDCMImageIO.h"
> > #include "itkVersion.h"
> > #include "itkOrientedImage.h"
> > #include "itkMinimumMaximumImageFilter.h"
> > #include "itkGDCMImageIO.h"
> > #include "itkGDCMSeriesFileNames.h"
> > #include "itkNumericSeriesFileNames.h"
> > #include "itkImageSeriesReader.h"
> > #include "itkImageSeriesWriter.h"
> > #include "itkResampleImageFilter.h"
> > #include "itkShiftScaleImageFilter.h"
> > #include "itkIdentityTransform.h"
> > #include "itkLinearInterpolateImageFunction.h"
> > #include <itksys/SystemTools.hxx>
> > #include "gdcm/src/gdcmFile.h"
> > #include "gdcm/src/gdcmUtil.h"
> > #include <string>
> > int main( int argc, char *argv[])
> > {
> > if( argc < 7 )
> > {
> > std::cerr << "Missing Parameters " << std::endl;
> > std::cerr << "Usage: " << argv[0];
> > std::cerr << " inputImage outputImage seedX seedY seedZ
> lowerThreshold
> > upperThreshold" << std::endl;
> > return 1;
> > }
> > typedef float InternalPixelType;
> >
> > const unsigned int Dimension = 3;
> > typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
> > typedef signed short OutputPixelType;
> > typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
> > typedef itk::Image< float, Dimension > OutputImageType2;
> > typedef itk::CastImageFilter< InternalImageType, OutputImageType >
> > CastingFilterType;
> > CastingFilterType::Pointer caster = CastingFilterType::New();
> >
> > const unsigned int ImageDimension = 3;
> > typedef signed short PixelType;
> > typedef itk::Image< PixelType, ImageDimension > FixedImageType;
> > typedef itk::Image< float, ImageDimension > FloatImageType;
> > typedef itk::ImageFileReader< FixedImageType > ReaderType;
> > typedef itk::ImageFileWriter< OutputImageType > WriterType;
> > typedef itk::ImageFileWriter< FloatImageType > WriterType2;
> > ReaderType::Pointer reader = ReaderType::New();
> > WriterType::Pointer writer = WriterType::New();
> > WriterType2::Pointer writer2 = WriterType2::New();
> > typedef itk::GDCMImageIO ImageIOTypefixed;
> > ImageIOTypefixed::Pointer gdcmImageIOfixed = ImageIOTypefixed::New();
> > reader->SetImageIO( gdcmImageIOfixed );
> > typedef itk::GDCMImageIO ImageIOTypefixed2;
> > ImageIOTypefixed2::Pointer gdcmImageIOfixed2 =
> ImageIOTypefixed2::New();
> > reader->SetFileName( argv[1] );
> > reader->Update();
> > typedef itk::CurvatureFlowImageFilter< InternalImageType,
> > InternalImageType >
> > CurvatureFlowImageFilterType;
> >
> > CurvatureFlowImageFilterType::Pointer smoothing =
> > CurvatureFlowImageFilterType::New();
> > typedef itk::ConnectedThresholdImageFilter< InternalImageType,
> > InternalImageType >
> ConnectedFilterType;
> > ConnectedFilterType::Pointer connectedThreshold =
> > ConnectedFilterType::New();
> > typedef signed short InputAPixelType;
> > typedef float OutputBPixelType;
> > typedef itk::Image< InputAPixelType, 3 > InputAImageType;
> > typedef itk::Image< OutputBPixelType, 3 > OutputBImageType;
> > typedef itk::CastImageFilter< InputAImageType, OutputBImageType >
> > CastFilterType;
> > CastFilterType::Pointer castFilter = CastFilterType::New();
> > castFilter->SetInput( reader->GetOutput() );
> >
> > connectedThreshold->SetInput( castFilter->GetOutput() );
> > caster->SetInput( connectedThreshold->GetOutput() );
> > smoothing->SetNumberOfIterations( 20 ); //was 5
> > smoothing->SetTimeStep( 0.125 );
> >
> > const InternalPixelType lowerThreshold = atof( argv[6] );
> > const InternalPixelType upperThreshold = atof( argv[7] );
> >
> > connectedThreshold->SetLower( lowerThreshold );
> > connectedThreshold->SetUpper( upperThreshold );
> >
> > connectedThreshold->SetReplaceValue( 255 );
> > InternalImageType::IndexType index;
> >
> > index[0] = atoi( argv[3] );
> > index[1] = atoi( argv[4] );
> >
> > //added
> > index[2] = atoi( argv[5] );
> > std::cout << index << std::endl;
> > // Software Guide : BeginCodeSnippet
> > connectedThreshold->SetSeed( index );
> >
> > //obtain a 5 x 5 bounding region of seeds
> > int ii, jj, kk;
> > ii = index[0];
> > jj = index[1];
> > kk = index[2];
> > for (int i = ii; i < ii + 5; i++)
> > for (int j = jj; j < jj + 5; j++)
> > for (int k = kk; k < kk + 5; k++)
> > {
> >
> > index[0] = i;
> > index[1] = j;
> > index[2] = k;
> > connectedThreshold->AddSeed( index );
> > }
> > for (int i = ii; i > ii - 5; i--)
> > for (int j = jj; j > jj - 5; j--)
> > for (int k = kk; k > kk - 5; k--)
> > {
> >
> > index[0] = i;
> > index[1] = j;
> > index[2] = k;
> > connectedThreshold->AddSeed( index );
> > }
> > connectedThreshold->Print(std::cout,17100);
> >
> > typedef itk::MetaDataDictionary DictionaryType;
> >
> > DictionaryType inputdict = reader->GetMetaDataDictionary();
> >
> > writer->SetMetaDataDictionary( inputdict );
> >
> > writer->SetFileName( argv[2] );
> >
> > writer->SetInput( caster->GetOutput() );
> > try
> > {
> > writer->Update();
> > }
> > catch( itk::ExceptionObject & excep )
> > {
> > std::cerr << "Exception caught !" << std::endl;
> > std::cerr << excep << std::endl;
> > }
> > return 0;
> > On Fri, Nov 27, 2009 at 12:31 PM, John Drozd <john.drozd at gmail.com>
> wrote:
> >>
> >> Hi all,
> >>
> >> I originally have a dicom series of 2d slices which I had converted to a
> >> 3D dicom volume for processing.
> >> I'll try processing the dicom series and then write the output to a
> dicom
> >> series of 2d slices, to see if I can circumvent this problem.
> >> I'll let you know if this works?
> >>
> >> I'll provide a link to my data as well, but it probably won't be until
> the
> >> weekend.
> >>
> >> Thanks,
> >> john
> >>
> >> On Fri, Nov 27, 2009 at 12:23 PM, Mathieu Malaterre
> >> <mathieu.malaterre at gmail.com> wrote:
> >>>
> >>> This is a post ITK 3.16 feature I am afraid:
> >>>
> >>> http://www.cmake.org/Bug/view.php?id=7748
> >>>
> >>> (0017626)
> >>> Mathieu.Malaterre (developer)
> >>> 2009-09-19 06:51
> >>>
> >>> This will be post ITK 3.16.
> >>>
> >>> Thanks for the patch ! Sorry for being so long to fix it.
> >>>
> >>> On Fri, Nov 27, 2009 at 6:11 PM, Bill Lorensen <
> bill.lorensen at gmail.com>
> >>> wrote:
> >>> > John,
> >>> >
> >>> > 3.16 will not help. This looks like a bug for sure.
> >>> >
> >>> > Can you provide a link to a dataset that we can use to reproduce the
> >>> > problem? We don't have much experience with 3D dicom files I'm
> afraid.
> >>> >
> >>> > Bill
> >>> >
> >>> > On Fri, Nov 27, 2009 at 11:59 AM, John Drozd <john.drozd at gmail.com>
> >>> > wrote:
> >>> >> Hi Bill,
> >>> >>
> >>> >> I am currently using the ITK 3.14 that is in the 3D Slicer 3.4
> >>> >> directory Slicer3-lib/Insight
> >>> >>
> >>> >> If I upgrade to ITK 3.16, will this solve my problem?
> >>> >>
> >>> >> I downloaded ITK 3.16 and noticed using the diff command that
> >>> >> itkGDCMIO.h has been modified from what it was in ITK 3.14.
> >>> >>
> >>> >> But when I ran diff on gdcmOrientation.cxx in both versions of ITK,
> >>> >> diff showed no difference.
> >>> >>
> >>> >> John
> >>> >>
> >>> >> On Friday, November 27, 2009, Bill Lorensen <
> bill.lorensen at gmail.com>
> >>> >> wrote:
> >>> >>> John,
> >>> >>>
> >>> >>> What version of itk are you using? Are you using the gdcm 1.x that
> is
> >>> >>> in the itk source tree or an external gdcm 2.x version?
> >>> >>>
> >>> >>> Bill
> >>> >>>
> >>> >>> On Thu, Nov 26, 2009 at 3:22 PM, John Drozd <john.drozd at gmail.com>
> >>> >>> wrote:
> >>> >>>> Hi Luis,
> >>> >>>>
> >>> >>>> I was getting a segmentation fault because I had forgotten to
> change
> >>> >>>> the
> >>> >>>> Dimension from 2 to 3 in DicomReadPrintTag.cxx.
> >>> >>>>
> >>> >>>> For the input image, I have:
> >>> >>>> (0020|0037) Image Orientation (Patient) = 0.0\0.0\-1.0\0.0\1.0\0.0
> >>> >>>>
> >>> >>>> For the output image, I have:
> >>> >>>> (0020|0037) Image Orientation (Patient) =
> >>> >>>> 0.000000\0.000000\1.000000\0.000000\1.000000\0.000000
> >>> >>>>
> >>> >>>> There is a difference. Since the program is changing the
> >>> >>>> orientation when
> >>> >>>> processed through the pipeline, is the best approach to manually
> >>> >>>> change the
> >>> >>>> orientation tag of the dictionary and then copy the revised
> >>> >>>> dictionary to
> >>> >>>> the output file?
> >>> >>>>
> >>> >>>> john
> >>> >>>>
> >>> >>>> Below are the full tags:
> >>> >>>>
> >>> >>>> [jdrozd at trumpet DicomImageReadPrintTags]$
> ./DicomImageReadPrintTags
> >>> >>>> correctedsubject5.dcm
> >>> >>>> (0002|0000) Group Length =
> >>> >>>> 214
> >>> >>>> (0002|0001) File Meta Information Version =
> >>> >>>> AAE=
> >>> >>>> (0002|0002) Media Storage SOP Class UID =
> >>> >>>> 1.2.840.10008.5.1.4.1.1.2
> >>> >>>> (0002|0003) Media Storage SOP Instance UID =
> >>> >>>> 1.2.826.0.1.3680043.2.1125.1.10607669833050788267094246636093811
> >>> >>>> (0002|0010) Transfer Syntax UID =
> >>> >>>> 1.2.840.10008.1.2.1
> >>> >>>> (0002|0012) Implementation Class UID =
> >>> >>>> 147.144.143.155
> >>> >>>> (0002|0013) Implementation Version Name = ITK/GDCM
> >>> >>>> 1.2.4
> >>> >>>> (0002|0016) Source Application Entity Title =
> >>> >>>> NOTSPECIFIED
> >>> >>>> (0008|0008) Image Type =
> >>> >>>> DERIVED\PRIMARY
> >>> >>>> (0008|0012) Instance Creation Date =
> >>> >>>> 20091029
> >>> >>>> (0008|0013) Instance Creation Time =
> >>> >>>> 135224
> >>> >>>> (0008|0016) SOP Class UID =
> >>> >>>> 1.2.840.10008.5.1.4.1.1.2
> >>> >>>> (0008|0018) SOP Instance UID =
> >>> >>>> 1.2.826.0.1.3680043.2.1125.1.10607669833050788267094246636093811
> >>> >>>> (0008|0020) Study Date =
> >>> >>>> 20081030
> >>> >>>> (0008|0030) Study Time =
> >>> >>>> 164348.940
> >>> >>>> (0008|0050) Accession Number
> >>> >>>> =
> >>> >>>> (0008|0060) Modality =
> >>> >>>> CT
> >>> >>>> (0008|0064) Conversion Type =
> >>> >>>> WSD
> >>> >>>> (0008|0070) Manufacturer =
> >>> >>>> Manifacturer
> >>> >>>> (0008|0080) Institution Name = GDCM
> >>> >>>> Hospital
> >>> >>>> (0008|0090) Referring Physician's Name = Refering
> >>> >>>> Phisician
> >>> >>>> (0010|0010) Patient's Name = Patient
> >>> >>>> 188858520
> >>> >>>> (0010|0020) Patient ID =
> >>> >>>> 1747233212
> >>> >>>> (0010|0030) Patient's Birth Date =
> >>> >>>> 19500101
> >>> >>>> (0010|0040) Patient's Sex =
> >>> >>>> M
> >>> >>>> (0018|0088) Spacing Between Slices =
> >>> >>>> 1.207500
> >>> >>>> (0018|1164) Imager Pixel Spacing =
> >>> >>>> 0.945750\0.945750
> >>> >>>> (0020|000d) Study Instance UID =
> >>> >>>> 1.2.826.0.1.3680043.2.1125.1.53653479342656887425609263146205769
> >>> >>>> (0020|000e) Series Instance UID =
> >>> >>>> 1.2.826.0.1.3680043.2.1125.1.47155241092896696198844159625679986
> >>> >>>> (0020|0010) Study ID =
> >>> >>>> 1533117581
> >>> >>>> (0020|0011) Series Number =
> >>> >>>> 2135500125
> >>> >>>> (0020|0013) Instance Number =
> >>> >>>> 165
> >>> >>>> (0020|0020) Patient Orientation =
> >>> >>>> L\P
> >>> >>>> (0020|0032) Image Position (Patient) =
> >>> >>>> 199.237496852874\0.0\0.0
> >>> >>>> (0020|0037) Image Orientation (Patient) =
> >>> >>>> 0.0\0.0\-1.0\0.0\1.0\0.0
> >>> >>>> (0020|4000) Image Comments = NOT FOR CLINICAL
> >>> >>>> USE
> >>> >>>> (0028|0002) Samples per Pixel =
> >>> >>>> 1
> >>> >>>> (0028|0004) Photometric Interpretation =
> >>> >>>> MONOCHROME2
> >>> >>>> (0028|0008) Number of Frames =
> >>> >>>> 166
> >>> >>>> (0028|0010) Rows =
> >>> >>>> 256
> >>> >>>> (0028|0011) Columns =
> >>> >>>> 256
> >>> >>>> (0028|0030) Pixel Spacing =
> >>> >>>> 0.945750\0.945750
> >>> >>>> (0028|0034) Pixel Aspect Ratio =
> >>> >>>> 1\1
> >>> >>>> (0028|0100) Bits Allocated =
> >>> >>>> 16
> >>> >>>> (0028|0101) Bits Stored =
> >>> >>>> 16
> >>> >>>> (0028|0102) High Bit =
> >>> >>>> 15
> >>> >>>> (0028|0103) Pixel Representation =
> >>> >>>> 0
> >>> >>>> (0028|1052) Rescale Intercept =
> >>> >>>> 0.0
> >>> >>>> (0028|1053) Rescale Slope =
> >>> >>>> 1.0
> >>> >>>> (0028|1054) Rescale Type =
> >>> >>>> US
> >>> >>>> (7fe0|0000) Group Length =
> >>> >>>> 21757964
> >>> >>>> Patient's Name (0010|0010) is: Patient
> >>> >>>> 188858520
> >>> >>>> Performing Physician's Name (0008|1050): (No Value Found in
> >>> >>>> File)
> >>> >>>> PixelType:
> >>> >>>> scalar
> >>> >>>> Component Type: unsigned_short
> >>> >>>>
> >>> >>>> [jdrozd at trumpet DicomImageReadPrintTags]$
> ./DicomImageReadPrintTags
> >>> >>>> outsubject5.dcm
> >>> >>>> (0002|0000) Group Length =
> >>> >>>> 194
> >>> >>>> (0002|00
> >>> >>
> >>> > _____________________________________
> >>> > Powered by www.kitware.com
> >>> >
> >>> > Visit other Kitware open-source projects at
> >>> > http://www.kitware.com/opensource/opensource.html
> >>> >
> >>> > Kitware offers ITK Training Courses, for more information visit:
> >>> > http://www.kitware.com/products/protraining.html
> >>> >
> >>> > Please keep messages on-topic and check the ITK FAQ at:
> >>> > http://www.itk.org/Wiki/ITK_FAQ
> >>> >
> >>> > Follow this link to subscribe/unsubscribe:
> >>> > http://www.itk.org/mailman/listinfo/insight-users
> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Mathieu
> >>
> >
> >
>
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