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</o:shapelayout></xml><![endif]--></head><body lang=DE-CH link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Hello everybody,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>I’m facing a problem regarding the manipulation of the Meta Data Dictionary in DICOM files:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>The task is to register/resample a DICOM series. Based on this, the number of slides changes. So each slide dictionary has to be processed as well. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>The array with the new information is passed over to the writer by the following function:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US> writer->SetMetaDataDictionaryArray(&outputArray).<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>The function corrupts the series somehow, so that the z-Voxel spacing/Coordinates are wrong. (ITK-SNAP just puts 1).<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Even if I just read and write the DICOM-Series and use this function, the failure appears:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>seriesWriter->SetInput(reader</span><span lang=EN-US>-></span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>GetOutput());<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>seriesWriter->SetMetaDataDictionaryArray( reader->GetMetaDataDictionaryArray());</span><span lang=EN-US><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>seriesWriter->Update();<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I tried to reread the corrupted series and resample it, but it did not worked: <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>reader: Original files.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>reader1: Corrupted series.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>seriesWriter1: Writer for the resampled image. (</span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>GetMetaDataDictionaryArray() not used</span><span lang=EN-US>)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:blue'>typedef</span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> itk::ResampleImageFilter <ImageType,ImageType> FilterType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>FilterType::Pointer filter=FilterType::New();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:blue'>typedef</span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> itk::AffineTransform < <span style='color:blue'>double</span>,3 > TransformType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>TransformType::Pointer transform = TransformType::New();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>transform->SetIdentity();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:blue'>typedef</span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> itk::NearestNeighborInterpolateImageFunction <ImageType, <span style='color:blue'>double</span> > InterpolatorType;<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>InterpolatorType::Pointer interpolator = InterpolatorType::New();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>ImageType *MoveImg=reader1->GetOutput();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>ImageType *FixImg=reader->GetOutput();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->SetInput(MoveImg);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:green'>/*filter->SetReferenceImage(FixImg);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:green'>filter->UseReferenceImageOn();*/<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:green'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>transform->SetIdentity();<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->SetTransform(transform);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:green'>//filter->SetInterpolator( interpolator );<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:green'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->SetDefaultPixelValue(0);<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->SetOutputSpacing(FixImg->GetSpacing());<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->SetOutputOrigin(FixImg->GetOrigin());<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->SetSize(FixImg->GetLargestPossibleRegion().GetSize());<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New";color:green'>//filter->SetOutputDirection(FixImg->GetDirection());<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>filter->Update();</span><span lang=EN-US><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'>seriesWriter1->SetInput(filter->GetOutput());<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I tried as well to set the spacing at the ImageIOType (</span><span lang=EN-US style='font-size:10.0pt;font-family:"Courier New"'>gdcmIO->SetSpacing(2,6.6)</span><span lang=EN-US>). Did not help.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>What I have found:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM">http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM</a> shows the error as well.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="https://itk.icts.uiowa.edu/jira/browse/ITK-182">https://itk.icts.uiowa.edu/jira/browse/ITK-182</a> Is there a batch or work around ??<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Some search results:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2008-November/027993.html">http://www.itk.org/pipermail/insight-users/2008-November/027993.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2005-September/014908.html">http://www.itk.org/pipermail/insight-users/2005-September/014908.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2005-August/014314.html">http://www.itk.org/pipermail/insight-users/2005-August/014314.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2010-January/035020.html">http://www.itk.org/pipermail/insight-users/2010-January/035020.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2008-June/026238.html">http://www.itk.org/pipermail/insight-users/2008-June/026238.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2012-August/045600.html">http://www.itk.org/pipermail/insight-users/2012-August/045600.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><a href="http://www.itk.org/pipermail/insight-users/2010-April/036334.html">http://www.itk.org/pipermail/insight-users/2010-April/036334.html</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Thank you in advance.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Best Regards<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Thomas<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></body></html>