[Insight-users] Problem generating a 3D volume from a set of slices

Dora Szasz dora.szasz at yahoo.com
Wed May 18 10:12:20 EDT 2011 

Yes. Exactly the same one.


________________________________
From: Bill Lorensen <bill.lorensen at gmail.com>
To: Dora Szasz <dora.szasz at yahoo.com>
Cc: "insight-users at itk.org" <insight-users at itk.org>
Sent: Wednesday, May 18, 2011 5:06 PM
Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices


Do you get the same exception message?


On Wed, May 18, 2011 at 9:07 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:

It writes me the name of the files, but no .mhd ouput file.
>
>
>File: Dora0001.png
>File: Dora0002.png
>File: Dora0003.png
>File: Dora0004.png
>File: Dora0005.png
>
>
>
>________________________________
>From: Bill Lorensen <bill.lorensen at gmail.com>
>To: Dora Szasz <dora.szasz at yahoo.com>
>Cc: Insight-Users <insight-users at itk.org>
>Sent: Wednesday, May 18, 2011 3:27 PM
>
>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>
>
>
>[please keep the mailing list involved]
>Try printing out the generated filenames. Something like:
>
>  std::vector<std::string> names = nameGenerator->GetFileNames();
>  std::vector<std::string>::iterator nit;
>
>  for (nit = names.begin();
>       nit != names.end();
>       nit++)
>    {
>    std::cout << "File: " << (*nit).c_str() << std::endl;
>    }
>
>
>
>
>
>On Wed, May 18, 2011 at 8:16 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>
>I've tried all the possibilities. Even if I run BrainModel.exe 1 5 out.mhd the error appears and I don't know why.
>>
>>
>>
>>________________________________
>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>To: Dora Szasz <dora.szasz at yahoo.com>
>>Cc: Insight-Users <insight-users at itk.org>
>>Sent: Wednesday, May 18, 2011 3:00 PM
>>
>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>
>>
>>
>>But the program should be run as:
>>BrainModel.exe 1 5 out.mhd
>>
>>at least according to the source you attached.
>>
>>
>>On Wed, May 18, 2011 at 2:00 AM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>
>>Hi Bill,
>>>
>>>
>>>Yes, the names of the files are correct, but the following  error message appears:
>>>I have verified and the size of the pictures is the same. I don't know what could be the problem.
>>>Thank you!
>>>
>>>
>>>D:\Lib\Project\Dora\bin\Debug>BrainModel.exe Dora0001d.png Dora0005d.png out.mhd
>>>ExceptionObject caught !
>>>
>>>
>>>itk::ExceptionObject (00B2F4D8)
>>>Location: "void __thiscall itk::ImageFileWriter<class itk::Image<unsigned char,3
>>>> >::Write(void)"
>>>File: d:\lib\_itk\source\code\io\itkImageFileWriter.txx
>>>Line: 271
>>>Description: itk::ERROR: ImageFileWriter(0012F3F8): Largest possible region does
>>> not fully contain requested paste IO regionPaste IO region: ImageIORegion (00B2
>>>F910)
>>>  Dimension: 3
>>>  Index: 0 0 0
>>>  Size: 0 0 1
>>>Largest possible region: ImageRegion (00B2F9C4)
>>>  Dimension: 3
>>>  Index: [0, 0, 0]
>>>  Size: [0, 0, 1]
>>>
>>>
>>>
>>>________________________________
>>>From: Bill Lorensen <bill.lorensen at gmail.com>
>>>To: Dora Szasz <dora.szasz at yahoo.com>
>>>Cc: "insight-users at itk.org" <insight-users at itk.org>
>>>Sent: Wednesday, May 18, 2011 7:03 AM
>>>Subject: Re: [Insight-users] Problem generating a 3D volume from a set of slices
>>>
>>>
>>>
>>>Oops...
>>>Dora0001d.png
>>>Dora0002d.png
>>>Dora0003d.png
>>>...
>>>
>>>
>>>
>>>On Wed, May 18, 2011 at 12:02 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>>>
>>>What are the names of the file? From your code they should be something like:
>>>>Dora00001d.png
>>>>Dora00002d.png
>>>>Dora00003d.png
>>>>...
>>>>
>>>>Is that how your files are named?
>>>>
>>>>Bill
>>>>
>>>>
>>>>On Tue, May 17, 2011 at 4:19 PM, Dora Szasz <dora.szasz at yahoo.com> wrote:
>>>>
>>>>Hello all,
>>>>>
>>>>>
>>>>>I am trying to make a 3D volume using a set of .png images. I want to obtain a 3D image (for example .mhd), but It doesn't generate any output.
>>>>>My code is the following:
>>>>>
>>>>>
>>>>>#include "itkImage.h"
>>>>> #include "itkImageSeriesReader.h"
>>>>> #include "itkImageFileWriter.h"
>>>>> #include "itkNumericSeriesFileNames.h"
>>>>> #include "itkPNGImageIO.h"
>>>>>
>>>>>
>>>>> int main( int argc, char ** argv )
>>>>> {
>>>>>  // Verify the number of parameters in the command line
>>>>>  if( argc < 4 )
>>>>>    {
>>>>>    std::cerr << "Usage: " << std::endl;
>>>>>    std::cerr << argv[0] << " firstSliceValue lastSliceValue outputImageFile " << std::endl;
>>>>>    return EXIT_FAILURE;
>>>>>    }
>>>>>
>>>>>
>>>>>  typedef unsigned char   PixelType;
>>>>>  const unsigned int Dimension = 3;
>>>>>
>>>>>
>>>>>  typedef itk::Image< PixelType, Dimension >  ImageType;
>>>>>  typedef itk::ImageSeriesReader< ImageType >  ReaderType;
>>>>>  typedef itk::ImageFileWriter<   ImageType >  WriterType;
>>>>>
>>>>>
>>>>>  ReaderType::Pointer reader = ReaderType::New();
>>>>>  WriterType::Pointer writer = WriterType::New();
>>>>>
>>>>>
>>>>>  const unsigned int first = atoi( argv[1] );
>>>>>  const unsigned int last  = atoi( argv[2] );
>>>>>
>>>>>
>>>>>  const char * outputFilename = argv[3];
>>>>>
>>>>>
>>>>>  typedef itk::NumericSeriesFileNames    NameGeneratorType;
>>>>>
>>>>>
>>>>>  NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>>>>>
>>>>>
>>>>>  nameGenerator->SetSeriesFormat( "Dora00%02d.png" );
>>>>>
>>>>>
>>>>>  nameGenerator->SetStartIndex( first );
>>>>>  nameGenerator->SetEndIndex( last );
>>>>>  nameGenerator->SetIncrementIndex( 1 );
>>>>>
>>>>>
>>>>>  reader->SetImageIO( itk::PNGImageIO::New() );
>>>>>  reader->SetFileNames( nameGenerator->GetFileNames()  );
>>>>>
>>>>>
>>>>>  writer->SetFileName( outputFilename );
>>>>>  writer->SetInput( reader->GetOutput() );
>>>>>  try
>>>>>    {
>>>>>    writer->UpdateLargestPossibleRegion();
>>>>>        writer->Update();
>>>>>    }
>>>>>  catch( itk::ExceptionObject & err )
>>>>>    {
>>>>>    std::cerr << "ExceptionObject caught !" << std::endl;
>>>>>    std::cerr << err << std::endl;
>>>>>    return EXIT_FAILURE;
>>>>>    }
>>>>>  return EXIT_SUCCESS;
>>>>> }
>>>>>
>>>>>
>>>>>1. How could I modify it in order to obtain the volume?
>>>>>2. How could I modify it in order to use "itkImageToVTKImageFilter.h" to display it on vtk window?
>>>>>
>>>>>
>>>>>Thank you a lot!
>>>>>
>>>>>
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>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>>
>>
>
>
>
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