[Insight-users] read a meta image and write a volume to DICOM

[Andinet Enquobahrie]

Hello Wordon,

>1)if I want to read image using ImageFileReader<> directly,the
>GetMetaDataDictionaryArray can't use in writer.In this situation,how
>should I write the meta image to DICOM series as Luis said previously?
>  
>
GetMetaDataDictionaryArray() function is not available for image readers 
"not" pointing to an ImageIO class with MetaDataDictionary handling 
capability. For example, if you had a DICOM input image and you were 
using ImageSeriesReader pointing to GDCMImageIO, then you can access the 
MetaData array using GetMetaDataDictionaryArray function.

Anyways, for your situation, one thing you can do is to define an array 
of MetaDataDicitionary containing all DICOM relevant data and pass it to 
the ImagSeries writer using

ImageSeriesWriter::SetMetaDataDictionaryArray(YourMetaDataArray)


>2)If I can get the DICOM series,can I use the code as
>DicomSeriesReadImageWrite2.cxx to read series and write it to DICOM
>volume?
>
>          
>
Yes, you can use the example with a small modifcation to the image 
writing part of the code. "DicomSeriesReadImgeWrite2" writes out the 
image in a different format other than DICOM. All you need to do is to 
use an image series file writer with a pointer to GDCMImageIO.

typedef itk::ImageSeriesWriter< ImageType, Image2DType > WriterType;
WriterType::Pointer writer = WriterType::New();

typedef itk::GDCMImageIO	ImageIOType;
ImageIOType::Pointer gdcmImageIO=ImageIOType::New();

writer->SetImageIO(gdcmImageIO);
writer->SetInput( reader->GetOutput() );  

...then specify filenames to the image series writer...


-Andinet

  



typedef itk::Image

>                                                        
>  
>




-Andinet

>
>2005/9/16, Luis Ibanez <luis.ibanez at kitware.com>:
>  
>
>>Hi Wordon,
>>
>>1) Yes, it is correct to read a MetaImage with just an ImageFileReader<>
>>
>>2) No, it is not right to write a volume as a DICOM file by using only
>>    the ImageFileWriter.  You MUST use the ImageSeriesWriter as explained
>>    in detail in the ITK Software Guide
>>
>>        http://www.itk.org/ItkSoftwareGuide.pdf
>>
>>    in the Chapter "Reading and Writing Images".
>>
>>    Note that you must also connect the GDCMImageIO.
>>
>>    You will find the relevant source code examples in the directory
>>
>>                 Insight/Examples/IO
>>
>>
>>3) A Series is when you store an N-Dimensional image by using
>>    multiple files that have dimensions inferior to N.
>>    The typical case is to use many 2D files for saving the slices
>>    of a 3D volume.
>>
>>    It is also common to have many 3D files for saving a 4D image,
>>    like for functional MRI, or PET studies, or Cardiac CT
>>
>>    With ITK you can write an N-Dimensional image as a series of
>>    files with image of Dimension M, where M < N.
>>
>>
>>4) If you store a volume (a 3D image) in DICOM, it will be stored
>>    in a series of 2D images.
>>
>>
>>Please read the ITK Software Guide,
>>
>>
>>    Regards,
>>
>>
>>       Luis
>>
>>
>>----------------------------
>>陳政煒 wrote:
>>    
>>
>>>Hi,Luis and all ITK user:
>>>
>>>I want to read a meta image and use the data '
>>>BrainProtonDensity3Slices.mha' & ' BrainProtonDensity3Slices.raw ' in
>>>Insight\Examples\Data.
>>>( I want to read a 3D raw image )
>>>
>>>And then wirte the meta image  into a volume of DICOM format.
>>>(.mhd or .mha --> .dcm)
>>>
>>>
>>>My code as follows :
>>>
>>>#include "itkImageFileReader.h"
>>>#include "itkImageFileWriter.h"
>>>#include "itkImage.h"
>>>#include "itkRescaleIntensityImageFilter.h"
>>>#include "itkMetaDataDictionary.h"
>>>#include "itkMetaDataObject.h"
>>>#include "itkGDCMImageIO.h"
>>>
>>>#include <list>
>>>#include <fstream>
>>>
>>>int main(int ac, char* av[])
>>>{
>>>
>>>  if(ac < 3)
>>>    {
>>>    std::cerr << "Usage: " << av[0] << " InputMETAFile OutputDICOM\n";
>>>    return EXIT_FAILURE;
>>>    }
>>>
>>>  typedef itk::Image<unsigned char, 3> ImageType;
>>>
>>>  typedef itk::ImageFileReader< ImageType > VolumeReaderType;
>>>
>>>  VolumeReaderType::Pointer reader = VolumeReaderType::New();
>>>
>>>  reader->SetFileName( av[1] );
>>>
>>>  try
>>>    {
>>>    reader->Update();
>>>    }
>>>  catch (itk::ExceptionObject & e)
>>>    {
>>>    std::cerr << "exception in file reader " << std::endl;
>>>    std::cerr << e.GetDescription() << std::endl;
>>>    std::cerr << e.GetLocation() << std::endl;
>>>    return EXIT_FAILURE;
>>>    }
>>>
>>>
>>>  typedef itk::GDCMImageIO        ImageIOType;
>>>
>>>  ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
>>>
>>>
>>>  typedef itk::Image<unsigned char, 3> WriteType;
>>>  typedef itk::ImageFileWriter<WriteType>     Writer1Type;
>>>  Writer1Type::Pointer writer1=Writer1Type::New();
>>>
>>>  writer1->SetFileName( av[2] );
>>>  writer1->SetImageIO( gdcmImageIO );
>>>  writer1->SetInput( reader->GetOutput() );
>>>
>>>
>>>  try
>>>    {
>>>    writer1->Update();
>>>    }
>>>  catch (itk::ExceptionObject & e)
>>>    {
>>>    std::cerr << "exception in file writer " << std::endl;
>>>    std::cerr << e.GetDescription() << std::endl;
>>>    std::cerr << e.GetLocation() << std::endl;
>>>    return EXIT_FAILURE;
>>>    }
>>>
>>>
>>>
>>>  return EXIT_SUCCESS;
>>>
>>>}
>>>
>>>My code can run,but the DICOM image in output is not correctly.
>>>It has a problem like loss some information in output file.
>>>
>>>My questions:
>>>1)Is it right to read the 3D meta image use ImageFileReader directly?
>>>2)Is it right to write the data into a volume of DICOM use
>>>ImageFileWriter directly?
>>>3)What are difference between series and volume?
>>>4)If I want to get a 3D DICOM file in one file.Is it a volume?
>>>
>>>Thanks a lot. : -)
>>>                                                              Wordon
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
>>>
>>>
>>>      
>>>
>>
>>    
>>
>>------------------------------------------------------------------------
>>
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>>Insight-users at itk.org
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>>    
>>