[Insight-users] Problem generating a 3D volume from a set of slices
Dora Szasz
dora.szasz at yahoo.com
Wed May 18 09:07:44 EDT 2011
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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