[ITK] [ITK-users] Image conversion from 3D volume to 2D slices

[Dženan Zukić]

Definitions of RescaleFilterType and FilterType should be like this:

typedef itk::RescaleIntensityImageFilter< InputImageType, OutputImageType >
RescaleFilterType;
typedef itk::ExtractImageFilter< OutputImageType, OutputImageType >
FilterType;

On Wed, May 8, 2019 at 1:54 PM Shrabani Ghosh <srbn.ghosh99 at gmail.com>
wrote:

> I did it like this and I am getting images like this now.
> <http://itk-insight-users.2283740.n2.nabble.com/file/t396636/slice1.png>
>
>
>
> int main( int argc, char ** argv )
> {
>
>   //typedef signed short        InputPixelType;
>   /*typedef unsigned char       InputPixelType;
>   typedef unsigned char        OutputPixelType;*/
>   typedef signed short       InputPixelType;
>   typedef unsigned char      OutputPixelType;
>   typedef itk::Image< InputPixelType,  3 >    InputImageType;
>   typedef itk::Image< OutputPixelType, 2 >    OutputImageType;
>   typedef itk::ImageFileReader< InputImageType  >  ReaderType;
>   typedef itk::ImageFileWriter< OutputImageType >  WriterType;
>   const char * inputFilename  = "G:/My Drive/BMES2019/New
> folder/subject1.nii";
>
>   {
>                 int i = 1;
>
>                         std::string str="input//";
>                         std::string s1="slice";
>                         std::string s2 = std::to_string(i);
>                         std::string s3=".png";
>                         std::string s4=str+s1+s2+s3;
>                         const char *mycharp = s4.c_str();
>
>   const char * outputFilename = mycharp;
>
>   ReaderType::Pointer reader = ReaderType::New();
>   WriterType::Pointer writer = WriterType::New();
>
>   reader->SetFileName( inputFilename  );
>   writer->SetFileName( outputFilename );
>
>    typedef itk::RescaleIntensityImageFilter< InputImageType, InputImageType
> > RescaleFilterType;
>    RescaleFilterType::Pointer rescalefilter = RescaleFilterType::New();
>    rescalefilter->SetInput( reader->GetOutput() );
>
>   typedef itk::ExtractImageFilter< InputImageType,
>                                    OutputImageType > FilterType;
>   FilterType::Pointer filter = FilterType::New();
>   filter->InPlaceOn();
>   filter->SetDirectionCollapseToSubmatrix();
>    reader->UpdateOutputInformation();
>   InputImageType::RegionType inputRegion =
>            reader->GetOutput()->GetLargestPossibleRegion();
>
>   InputImageType::SizeType size = inputRegion.GetSize();
>   size[2] = 0;
>
>   InputImageType::IndexType start = inputRegion.GetIndex();
>   const unsigned int sliceNumber = stoi(s2);//atoi(argv[3]);
>   start[2] = sliceNumber;
>
>   InputImageType::RegionType desiredRegion;
>   desiredRegion.SetSize(  size  );
>   desiredRegion.SetIndex( start );
>
>   filter->SetExtractionRegion( desiredRegion );
>
>   filter->SetInput( rescalefilter->GetOutput() );
>   writer->SetInput( filter->GetOutput() );
>    try
>     {
>     writer->Update();
>     }
>   catch( itk::ExceptionObject & err )
>     {
>     std::cerr << "ExceptionObject caught !" << std::endl;
>     std::cerr << err << std::endl;
>         getchar();
>     return EXIT_FAILURE;
>     }
>     }
>   return EXIT_SUCCESS;
> }
>
>
>
> --
> Sent from: http://itk-insight-users.2283740.n2.nabble.com/
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