[Insight-users] Reading Analyze 7.5 images

[Luis Ibanez]

Hi  Ahmet,

You are probably generating an incorrect list of filenames.

Please do the following:

1) Remove the line:

       reader->SetImageIO( itk::AnalyzeImageIO::New() );

     The image IO factory should be able to find the appropriate
      ImageIO class for the file format that you are reading.

2)  Before calling reader->Update() print out all the filenames
      that result from the imageFileNameGenerator.

      You need to insert code such as:


    typedef std::vector<std::string> NamesContainerType;
    NamesContainerType  fileNames = nameGenerator->GetFileNames();

     NamesContainerType::const_iterator fitr = fileNames.begin();
     NamesContainerType::const_iterator fend = fileNames.fend();

     while( fitr != fend )
       {
       std::cout << *fitr << std::endl;
       ++fitr;
       }

3) Then you should verify that those names actually match existing files.
     You could do that manually, or you could use the following lines:

        #include <itksys/SystemTools.hxx>

        if(  !  SystemTools::FileExists(   *fitr )  )
          {
          std::cerr << "File " << *fitr << " does not exist " << std::endl;
          }


Please let us know what you find,


         Luis



---------------------------------------------------------
On Wed, Nov 11, 2009 at 4:27 AM, A.Burak Yoldemir <yoldemir at gmail.com> wrote:
> Hello Luis,
>
> I formerly sent an e-mail to insight-users group about a problem of mine
> which is about reading Analyze 7.5 images with ITK, but could not get a
> response. I am trying to read a set of images but getting a segmentation
> fault. I am copying my code and the output below. Do you have any
> suggestions?
>
>
> Code:
>             typedef unsigned char PixelType;
>             const unsigned int Dimension = 3;
>             typedef itk::Image< PixelType, Dimension > ImageType;
>
>             typedef itk::ImageSeriesReader< ImageType > ReaderType;
>
>             ReaderType::Pointer reader = ReaderType::New();
>
>             typedef itk::NumericSeriesFileNames    NameGeneratorType;
>             NameGeneratorType::Pointer nameGenerator =
> NameGeneratorType::New();
>
>
>             nameGenerator->SetSeriesFormat(
> "/root/Desktop/default_10-v1.0.3/default_10-v1.0.3/phantom_01/clean/dwi-%02d.hdr"
> );
>
>             nameGenerator->SetStartIndex( 0 );
>             nameGenerator->SetEndIndex( 66 );
>             nameGenerator->SetIncrementIndex( 1 );
>
>             reader->SetImageIO( itk::AnalyzeImageIO::New() );
>
>             reader->SetFileNames( nameGenerator->GetFileNames() );
>
>             cout << "Before try/catch" << endl;
>             try
>             {
>                 cout << "Try1" << endl;
>                 reader->Update();
>                 cout << "Try2" << endl;
>             }
>             catch (itk::ExceptionObject &e)
>             {
>                 std::cerr << e << std::endl;
>                 return EXIT_FAILURE;
>             }
>
>
> Output:
> Before try/catch
> Try1
> Segmentation fault
>
>
> Thanks in advance,
>
> Ahmet Burak Yoldemir
>