[Insight-users] Re: DICOM data reading

[Luis Ibanez]

Hi Martin,

It is quite common to have multiple DICOM series in
the same directory.  The way to select the series is
therefore to make a first pass to your directory and
to collect the list of series that are present, along
with additional patient information such as name, sex
and age.


In a typical application, this list will be presented
to the user, who will select to read one of the series
from that list.

Once you have a series ID, the series can be passed to
the GDCMSeriesFileNames in order to generate the file
names of only the slices that belong to the selected
series.

All this is described in detail in the ITK Software Guide


      http://www.itk.org/ItkSoftwareGuide.pdf

in Chapter 7, "Reading and Writing Images". In particular
in section 7.12.3, in pdf-page 324.


Note that for gathering all the series in a directory
you use the GDCMSeriesFileNames class and pass to it the
directory using the method

                SetDirectory()

Then you get the list of Series IDs with the method

                GetSeriesUIDs()

at this point you present this list to a User, probably
using a GUI, and let the user select the series that
she wants to read. Then you pass that series Id to the
same GDCMSeriesFileNames generator using the method:

               GetFileNames( seriesUID )

The list of filenames is finally passed to the
ImageSeriesReader, and at that point you can trigger
the process of reading all the slices.

The source code example that describes this same process
is available in


          Insight/Examples/IO/
              DicomSeriesReadImageWrite2.cxx




For an example of how this is done in a GUI, please look
at the application developed by the ISIS Center at Georgetown
University, that is available in


        InsightApplications/
                  LiverTumorSegmentation


In the "File" menu of this application you will find an option
for "Load DICOM". This options does what has been described
above.



Please let us know if you have further questions,


     Regards,



        Luis



--------------------------------
Martin SEISER wrote:

> Dear Mr. Ibanez,
> 
> my name is Martin Seiser and i am currently working for the UMIT, the private medical informatics university, in Tyrol, Austria. My task is to read and writes series of DICOM data. I am using the 2.1.0 ITK api which offers a library to comforably get access to dicom data, which does work well for a single series. But there exists the possibility that there are multiple series in one folder and the user should have the possibility to choose, which data (chosen by patient ID or study ID) to load. That doesnt work at the moment, cause i have no clue if it works with my code. In my opinion I have to read the folder file by file and check each DICOM file for information used to choose series.
> 
> Here you have my code to read a folder:
> 
> int main(int argc, char* argv[]) {
> 	typedef itk::Image<unsigned short,3> ImageType;
> 	typedef itk::Image< unsigned char, 2 > Image2DType;
> 	typedef itk::ImageSeriesReader<ImageType> SeriesReaderType;
> 	typedef itk::ImageSeriesWriter<ImageType, Image2DType> SeriesWriterType;
> 	typedef itk::ImageFileWriter<ImageType> WriterType;
> 	typedef itk::GDCMImageIO ImageIOType;
> 	typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> 	typedef std::vector<std::string> fileNamesContainer;
> 	typedef itk::NumericSeriesFileNames NameGeneratorType;
> 
> 	if(argc < 4) {
> 		std::cerr << "Usage: " << argv[0] << " DicomDirectory  format extension  [seriesName]" << std::endl;
> 		return EXIT_FAILURE;
> 	}
> 
> 	ImageIOType::Pointer dicomIO = ImageIOType::New();
> 
> 	// Get the DICOM filenames from the directory
> 	NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
> 	nameGenerator->SetInputDirectory(argv[1]);
> 
> 	try {
> 		fileNamesContainer fileNames;
> 		fileNames = nameGenerator->GetInputFileNames();
> 		SeriesReaderType::Pointer reader = SeriesReaderType::New();
> 		reader->SetFileNames(fileNames);
> 		reader->SetImageIO(dicomIO);
> 
> 		try {
> 			reader->Update();
> 		}
> 		catch (itk::ExceptionObject &ex) {
> 			std::cout << ex << std::endl;
> 			return EXIT_FAILURE;
> 		}
> 
> 		char buffer[100];
> 
> 		dicomIO->GetPatientName(buffer);
> 		std::cout << "PatientName: " << buffer << std::endl;
> 		dicomIO->GetPatientID(buffer);
> 		std::cout << "PatientID: " << buffer << std::endl;
> 		dicomIO->GetPatientSex(buffer);
> 		std::cout << "PatientSex: " << buffer << std::endl;
> 		dicomIO->GetPatientAge(buffer);
> 		std::cout << "PatientAge: " << atoi(buffer) << std::endl;
> 		dicomIO->GetStudyID(buffer);
> 		std::cout << "StudyID: " << buffer << std::endl;
> 		dicomIO->GetNumberOfSeriesInStudy(buffer);
> 		std::cout << "NumberOfSeriesInStudy: " << atoi(buffer) << std::endl;
> 		dicomIO->GetNumberOfStudyRelatedSeries(buffer);
> 		std::cout << "NumberOfStudyRelatedSeries: " << atoi(buffer) << std::endl;
> 	}
> 	catch (itk::ExceptionObject &ex) {
> 		std::cout << ex << std::endl;
> 		return EXIT_FAILURE;
> 	}
> 	return EXIT_SUCCESS;
> }
> 
> And if I call the getter-methods above i only get the data of the first study read in!:(
> 
> Would be very glad if you could help me,
> 
> thx in advance
> 
> Martin Seiser
>