[Insight-users] creating a volume from separate slices

[Lucas Lorenzo]

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Thanks Josh,

I'm using the ImageSeriesReader.
The files are GE 5x (as far as I know the pixel type is unsigned int 16 
bit) so my understanding is that the IO factory mechanism should make 
it transparent for me the reading process. What I'd like to do is to 
generate the volume in Analyze format. I checked the generated list of 
file names and it's ok.
So, this is the code:

	#include "itkNumericSeriesFileNames.h"
	#include "itkImageSeriesReader.h"
	#include "itkImageFileWriter.h"
	#include "itkImage.h"
	#include "itkAnalyzeImageIO.h"
	#include <iostream>

	int main(int argc, char * argv[])
	{

	  typedef itk::Image<unsigned int,3> Image3DType;

	  typedef itk::AnalyzeImageIO ImageIOType;

	  ImageIOType::Pointer analyzeIO = ImageIOType::New();

	  //
	  // Here we generate filenames: I.001 I.002 ------ I.136
	  itk::NumericSeriesFileNames::Pointer fileIter = 
itk::NumericSeriesFileNames::New();
	  fileIter->SetStartIndex(   1 );
	  fileIter->SetEndIndex(   136 );
  	 fileIter->SetIncrementIndex( 1 );
  	 fileIter->SetSeriesFormat("I.%03d");

   	itk::ImageSeriesReader<Image3DType>::Pointer reader = 
itk::ImageSeriesReader<Image3DType>::New();
	  reader->SetFileNames( fileIter->GetFileNames() );

	  try
  	   {
  	     reader->Update();
  	   }
  	 catch( itk::ExceptionObject & err )
  	   {
   	    std::cout << "ExceptionObject caught !" << std::endl;
   	    std::cout << err << std::endl;
     	  return -1;
     	}


	  itk::ImageFileWriter< Image3DType >::Pointer writer = 
itk::ImageFileWriter< Image3DType >::New();
	  writer->SetInput(   reader->GetOutput()  );
	  writer->SetFileName("test");
	  writer->SetImageIO(analyzeIO);

   	try
   	  {
  	     writer->Update();
  	   }
	  catch( itk::ExceptionObject & err )
	    {
	      std::cout << "ExceptionObject caught !" << std::endl;
	      std::cout << err << std::endl;
  	     return -1;
  	   }
  	 return 0;
	}

but when doing the "reader->Update()" I have a run time error:

	ExceptionObject caught !

	itk::ExceptionObject (0x225c90)
	Location: "Unknown"
	File: /usr/local/include/InsightToolkit/IO/itkImageFileReader.txx
	Line: 101
	Description:  Could not create IO object for file I.002

So, it seems to be that it is reading the first file in the list 
("I.001") but it can't read the second.
Could anyone help me with this ?
Thanks

Lucas


On Thursday, November 6, 2003, at 11:07 AM, Joshua Cates wrote:

> Hi Lucas,
>
> To read slices into a volume, you can either create a MetaImageHeader 
> for
> it with the MetaImageImporter application, or use the
> itk::ImageSeriesReader.
>
> (if these are raw files, another trick is to 'cat' them into to a 
> single
> file)
>
> Josh.
> ______________________________
>  Josh Cates			
>  Scientific Computing and Imaging Institute
>  University of Utah
>  Email: cates at sci . utah . edu
>  Phone: (801) 587-7697
>  URL:   http://www . sci . utah . edu/~cates
>
>
> On Thu, 6 Nov 2003, Lucas Lorenzo wrote:
>
>> Hi,
>>
>> I have many slices (from a volume) stored in separate files.
>> How can I create the volume to save it to a file?
>> Thanks
>>
>> Lucas Lorenzo
>>
>> University of Utah
>> Nora Eccles Harrison CardioVascular Research and Training Institute
>> Fellows Room
>> 95 South 2000 East
>> Salt Lake City, UT 84112-5000
>>
>> e-mail:  lucas at cvrti . utah . edu
>> telephone: 801-587-9536
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk . org
>> http://www . itk . org/mailman/listinfo/insight-users
>>
>
>
Lucas Lorenzo

University of Utah
Nora Eccles Harrison CardioVascular Research and Training Institute
Fellows Room
95 South 2000 East
Salt Lake City, UT 84112-5000

e-mail:  lucas at cvrti . utah . edu
telephone: 801-587-9536

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Thanks Josh,


I'm using the ImageSeriesReader.

The files are GE 5x (as far as I know the pixel type is unsigned int
16 bit) so my understanding is that the IO factory mechanism should
make it transparent for me the reading process. What I'd like to do is
to generate the volume in Analyze format. I checked the generated list
of file names and it's ok.

So, this is the code:


<italic>	#include "itkNumericSeriesFileNames.h"

	#include "itkImageSeriesReader.h"

	#include "itkImageFileWriter.h"

	#include "itkImage.h"

	#include "itkAnalyzeImageIO.h"

	#include <<iostream>


	int main(int argc, char * argv[])

	{


	  typedef itk::Image<<unsigned int,3> Image3DType;

  

	  typedef itk::AnalyzeImageIO ImageIOType;


	  ImageIOType::Pointer analyzeIO = ImageIOType::New();


	  //

	  // Here we generate filenames: I.001 I.002 ------ I.136

	  itk::NumericSeriesFileNames::Pointer fileIter =
itk::NumericSeriesFileNames::New();

	  fileIter->SetStartIndex(   1 );

	  fileIter->SetEndIndex(   136 );

 	 fileIter->SetIncrementIndex( 1 );

 	 fileIter->SetSeriesFormat("I.%03d");


  	itk::ImageSeriesReader<<Image3DType>::Pointer reader =
itk::ImageSeriesReader<<Image3DType>::New();

	  reader->SetFileNames( fileIter->GetFileNames() );

  

	  try

 	   {

 	     reader->Update();

 	   }

 	 catch( itk::ExceptionObject & err )

 	   {

  	    std::cout <<<< "ExceptionObject caught !" <<<< std::endl;

  	    std::cout <<<< err <<<< std::endl;

    	  return -1;

    	}



	  itk::ImageFileWriter<< Image3DType >::Pointer writer =
itk::ImageFileWriter<< Image3DType >::New();

	  writer->SetInput(   reader->GetOutput()  );

	  writer->SetFileName("test");

	  writer->SetImageIO(analyzeIO);


  	try

  	  {

 	     writer->Update();

 	   }

	  catch( itk::ExceptionObject & err )

	    {

	      std::cout <<<< "ExceptionObject caught !" <<<< std::endl;

	      std::cout <<<< err <<<< std::endl;

 	     return -1;

 	   }

 	 return 0;

	}

</italic>

but when doing the "reader->Update()" I have a run time error: 


<italic>	ExceptionObject caught !


	itk::ExceptionObject (0x225c90)

	Location: "Unknown" 

	File: /usr/local/include/InsightToolkit/IO/itkImageFileReader.txx

	Line: 101

	Description:  Could not create IO object for file I.002</italic>


So, it seems to be that it is reading the first file in the list
("I.001") but it can't read the second.

Could anyone help me with this ?

Thanks


Lucas



On Thursday, November 6, 2003, at 11:07 AM, Joshua Cates wrote:


<excerpt>Hi Lucas,


To read slices into a volume, you can either create a MetaImageHeader
for

it with the MetaImageImporter application, or use the 

itk::ImageSeriesReader.


(if these are raw files, another trick is to 'cat' them into to a
single

file)


Josh.

______________________________

 Josh Cates			

 Scientific Computing and Imaging Institute

 University of Utah

 Email: cates at sci . utah . edu

 Phone: (801) 587-7697

 URL:   http://www . sci . utah . edu/~cates



On Thu, 6 Nov 2003, Lucas Lorenzo wrote:


<excerpt>Hi,


I have many slices (from a volume) stored in separate files.

How can I create the volume to save it to a file?

Thanks


Lucas Lorenzo


University of Utah

Nora Eccles Harrison CardioVascular Research and Training Institute

Fellows Room

95 South 2000 East

Salt Lake City, UT 84112-5000


e-mail:  lucas at cvrti . utah . edu

telephone: 801-587-9536


_______________________________________________

Insight-users mailing list

Insight-users at itk . org

http://www . itk . org/mailman/listinfo/insight-users


</excerpt>


</excerpt>Lucas Lorenzo


University of Utah

Nora Eccles Harrison CardioVascular Research and Training Institute

Fellows Room

95 South 2000 East

Salt Lake City, UT 84112-5000


e-mail:  lucas at cvrti . utah . edu

telephone: 801-587-9536


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