[Insight-users] Problem with saving Image Position value in "z" axis
Alberto
bertorey at gmail.com
Fri Apr 15 06:00:13 EDT 2011
Hi.
In my group are working with ITK 4 in order to detect ROIs in high
resolution CTs from LIDC database using fuzzy clustering algorithms.
We are having the same problem reported by Mr. Srna. When we write a DICOM
series the value of z in Image Patient Position (0020,0032) is always fixed
to zero, ignoring the correct value.
We tested this problem using the example DIcomSeriesReadSeriesWrite and the
result is the same reported.
We, also, debug the code and we believe the problem could be located in the
itkGDCMImageIO.cxx.
Can someone help with this problem?
Thanks in advance. All help is appreciated.
Best regards.
Alberto Rey
Dept. of Information and Communications Technologies
Faculty of Computer Science
University of A Coruna
2011/4/14 Bc. Michal Srna <michal at srna.info>
> Hello,
>
> I have used part of this code to generate MetaDataDictionary:
>
> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>
> Everything works, as I need, but I have just one problem in part regarding
> saving Image Position (origin) for "z" axis. "x,y" are stored well, but "z"
> value of Image Position is 0.
>
> Here is that part of the code for saving the Image position:
>
> ImageType::PointType position;
> ImageType::IndexType index;
> index[0] = 0;
> index[1] = 0;
> index[2] = f;
>
> reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);
>
> value.str("");
> value << position[0] << "\\" << position[1] << "\\"
> << position[2];
>
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str()); //WHY
> NOT WORKING??
>
> position[2] contains the correct value, but I don't know, why is that value
> not saved and instead of that value is stored just 0?
>
> I think I should add also the whole code for generating my
> MetaDataDictionary for see my problem in context.
>
> At first it opens original data, from which I read original meta data. Then
> I modify some parts of those meta data in for cycle creating meta data for
> each slice.
>
> I confirmed, that original data contains correct value of Image Position in
> "z" axis. But I need to recalculate that value and store new value. Problem
> is, as I told, that this value is not saved and instead of it, there is just
> 0.
>
> Here is the whole code, spacing[x] is derived from other part of the whole
> code, I don't want to copy here:
>
> /*opening original data for getting meta data dictionry for saving it into
> output 2D series files*/
> typedef itk::GDCMImageIO ImageIOType;
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> typedef itk::ImageSeriesReader< ImageType > ReaderType;
>
> ImageIOType::Pointer gdcmIO = ImageIOType::New();
> ReaderType::Pointer reader = ReaderType::New();
>
> NamesGeneratorType::Pointer namesGenerator =
> NamesGeneratorType::New();
> namesGenerator->SetInputDirectory( StudyFolderName );
> const ReaderType::FileNamesContainer & filenames =
> namesGenerator->GetInputFileNames();
>
> reader->SetImageIO( gdcmIO );
> reader->SetFileNames( filenames );
>
> reader->Update();
>
> /*creating MetaDataDictionary for each slice*/
>
> /*Copy the dictionary from the first image and override slice
> specific fields*/
> ReaderType::DictionaryRawPointer inputDictionary =
> (*(reader->GetMetaDataDictionaryArray()))[0];
> ReaderType::DictionaryArrayType dictionaryOutputArray;
>
> /*To keep the new series in the same study as the original we
> need to keep the same study UID. But we need new series and frame of
> reference UID's.*/
> #if ITK_VERSION_MAJOR >= 4
> gdcm::UIDGenerator suid;
> std::string seriesUID = suid.Generate();
> gdcm::UIDGenerator fuid;
> std::string frameOfReferenceUID = fuid.Generate();
> #else
> std::string seriesUID = gdcm::Util::CreateUniqueUID(
> gdcmIO->GetUIDPrefix());
> std::string frameOfReferenceUID =
> gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
> #endif
> std::string studyUID;
> std::string sopClassUID;
> itk::ExposeMetaData<std::string>(*inputDictionary,
> "0020|000d", studyUID);
> itk::ExposeMetaData<std::string>(*inputDictionary,
> "0008|0016", sopClassUID);
> gdcmIO->KeepOriginalUIDOn();
>
> for (unsigned int f = 0; f < size[2]; f++)
> {
> // Create a new dictionary for this slice
> ReaderType::DictionaryRawPointer dict = new
> ReaderType::DictionaryType;
>
> // Copy the dictionary from the first slice
> CopyDictionary (*inputDictionary, *dict);
>
> // Set the UID's for the study, series, SOP and frame
> of reference
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0052",
> frameOfReferenceUID);
>
> #if ITK_VERSION_MAJOR >= 4
> gdcm::UIDGenerator sopuid;
> std::string sopInstanceUID = sopuid.Generate();
> #else
> std::string sopInstanceUID =
> gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
> #endif
>
> itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);
>
> // Change fields that are slice specific
> itksys_ios::ostringstream value;
> value.str("");
> value << f + 1;
>
> // Image Number
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());
>
> // Series Description - Append new description to
> current series description
> std::string oldSeriesDesc;
> itk::ExposeMetaData<std::string>(*inputDictionary,
> "0008|103e", oldSeriesDesc);
>
> value.str("");
> value << oldSeriesDesc
> << spacing[0] << ", "
> << spacing[1] << ", "
> << spacing[2];
>
> // This is an long string and there is a 64 character
> limit in the standard
> unsigned lengthDesc = value.str().length();
>
> std::string seriesDesc( value.str(), 0,
> lengthDesc > 64 ? 64
> : lengthDesc);
>
> itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);
>
> // Series Number
> value.str("");
> value << 1001;
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());
>
> //Image Position Patient: This is calculated by
> computing the physical coordinate of the first pixel in each slice.
> ImageType::PointType position;
> ImageType::IndexType index;
> index[0] = 0;
> index[1] = 0;
> index[2] = f;
>
> reader->GetOutput()->TransformIndexToPhysicalPoint(index, position);
>
> value.str("");
> value << position[0] << "\\" << position[1] << "\\"
> << position[2];
>
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str()); //WHY
> NOT WORKING??
>
> // Slice Location: For now, we store the z component of
> the Image Position Patient.
> value.str("");
> value << position[2];
>
> itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());
>
> // Spacing Between Slices
> value.str("");
> value << spacing[2];
>
> itk::EncapsulateMetaData<std::string>(*dict,"0018|0088", value.str());
>
> // Change specific values
> // itk::EncapsulateMetaData<std::string>(*dict,
> "0028|0100", "16" );
>
>
> // Save the dictionary
> dictionaryOutputArray.push_back(dict);
> }
>
> Thanks guys in advance...
>
> --
> S pozdravem Bc. Michal Srna
>
> Fotografické portfolio:
> http://michalsrna.cz
>
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