[Insight-users] problem with orientation of dicom output from segmentation
Bill Lorensen
bill.lorensen at gmail.com
Fri Nov 27 16:59:06 EST 2009
Hmmm. Well if that turns out to be the case, we may have to patch
3.16. I'll look into this further this weekend.
Bill
On Fri, Nov 27, 2009 at 4:56 PM, Mathieu Malaterre
<mathieu.malaterre at gmail.com> wrote:
> I think this was post ITK 3.16 release...
>
> On Fri, Nov 27, 2009 at 10:48 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
>>>
>>> output volume from my ConnectedThresholdFilter code:
>>> http://www.apmaths.uwo.ca/~jdrozd/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:
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>>>>> >
>>>>> > Please keep messages on-topic and check the ITK FAQ at:
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>>>>> >
>>>>> > Follow this link to subscribe/unsubscribe:
>>>>> > http://www.itk.org/mailman/listinfo/insight-users
>>>>> >
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Mathieu
>>>>
>>>
>>>
>>
>
>
>
> --
> Mathieu
>
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