[Insight-users] read a meta image and write a volume to DICOM
wordon
m9421001 at gmail.com
Tue Sep 20 10:32:01 EDT 2005
Hi,Bill :
Thanks for your code.
I test it under VC6.0 and winXP command line,but has some problem.
1)It sometimes has error execution when I run the program.
ex:
>irdw headmrvolume.mhd t1
numberOfSlices: 42
file: t1.dcm1.dcm
file: t1.dcm2.dcm
.
.
.
file: t1.dcm32.dcm
file: t1.dcm33.dcm
-->In this time,the program has error execution.
My question is : Has any restrain in this program?
2)sometimes,the program can be run correctly.
ex:
>D:\play>irdw vhfcolor.mhd t11
numberOfSlices: 10
file: t111.dcm
file: t112.dcm
.
.
file: t119.dcm
file: t1110.dcm
(this step can run correctly)
But the series can not transform to a volume(.dcm) using fixed program
'DicomSeriesReadImageWrite2.cxx'.
The code for DicomSeriesReadImageWrite2.cxx is :
==================================================================
int main( int argc, char* argv[] )
{
if( argc < 3 )
{
std::cerr << "Usage: " << argv[0] << " DicomDirectory
outputFileName [seriesName]" << std::endl;
return EXIT_FAILURE;
}
typedef itk::Image<unsigned short,3> ImageType;
typedef itk::ImageSeriesReader< ImageType > ReaderType;
typedef itk::GDCMImageIO ImageIOType;
ImageIOType::Pointer dicomIO = ImageIOType::New();
// Get the DICOM filenames from the directory
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
nameGenerator->SetInputDirectory( argv[1] );
try
{
typedef std::vector<std::string> fileNamesContainer;
fileNamesContainer fileNames;
fileNames = nameGenerator->GetInputFileNames();
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileNames( fileNames );
reader->SetImageIO( dicomIO );
try
{
reader->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex << std::endl;
return EXIT_FAILURE;
}
typedef itk::ImageFileWriter< ImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
std::cout << "Writing the image as " << std::endl << std::endl;
std::cout << argv[2] << std::endl << std::endl;
writer->SetFileName( argv[2] );
writer->SetInput( reader->GetOutput() );
writer->SetImageIO( dicomIO );
try
{
writer->Update();
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex;
return EXIT_FAILURE;
}
}
catch (itk::ExceptionObject &ex)
{
std::cout << ex;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
=================================================================
Here,my question is : Has any loss information in the series?
Another,when I want to display the series or volume in VolView.
It has some error.
ex:
ERROR: In C:\kitware\VolView\VolView20\VolView\KWCommonPro\vtkDICOMCollector.cxx,
line 765
vtkDICOMCollector (0x0635D330): DICOM file [D:/play/tv]
=> missing required elements!
why is it?
Thanks a lot :-)
Wordon
在 2005/9/20，Lorensen, William E (Research) <lorensen at crd.ge.com> 撰寫：
>
>
> -----Original Message-----
> From: wordon [mailto:m9421001 at gmail.com]
> Sent: Monday, September 19, 2005 6:02 PM
> To: Lorensen, William E (Research)
> Cc: Andinet Enquobahrie; insight-users at itk.org
> Subject: Re: [Insight-users] read a meta image and write a volume to DICOM
>
>
> Hi,Bill:
>
> I need this code so immediately.
> Can you send me this code?
>
> Thank you very much. ; - )
>
> Wordon
>
>
> 2005/9/19, Lorensen, William E (Research) <lorensen at crd.ge.com>:
> > I have an Example that creates a valid dicom from a meta file. I still want to refine it before checking it into itk. If you have a need immediately, I can e-mail the code. It populates the meta dictionary with enough dicom to be acceptable for a GE Advantage Windows workstation. It also accepts tag/value pairs on the command line.
> >
> > Bill
> >
> > -----Original Message-----
> > From: insight-users-bounces+lorensen=crd.ge.com at itk.org
> > [mailto:insight-users-bounces+lorensen=crd.ge.com at itk.org]On Behalf Of
> > Andinet Enquobahrie
> > Sent: Monday, September 19, 2005 10:10 AM
> > To: m9421001 at gmail.com
> > Cc: insight-users at itk.org
> > Subject: Re: [Insight-users] read a meta image and write a volume to
> > DICOM
> >
> >
> > 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
> > >>>
> > >>>
> > >>>
> > >>>
> > >>
> > >>
> > >>
> > >>------------------------------------------------------------------------
> > >>
> > >>_______________________________________________
> > >>Insight-users mailing list
> > >>Insight-users at itk.org
> > >>http://www.itk.org/mailman/listinfo/insight-users
> > >>
> > >>
> >
> >
> > _______________________________________________
> > Insight-users mailing list
> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
>
>
>
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