[Insight-users] Problems with Analyze files

[Luis Ibanez]

Hi David,

There were a couple of problems with the Analyze
reader in the release 1.2.  These problems were
fixed after the release.

We are starting to prepare for release 1.4, which
should be available by september.



In the meantime, you may want to try one of the
following options:



1) Since the readers are relatively self-contained,
    you could try simply downloading the current
    version of the Analyze readers.

    You can easily do this through the CVS-Web interface:
http://www . itk . org/cgi-bin/cvsweb . cgi/Insight/Code/IO/?cvsroot=Insight


2) You could move to fully use the CVS version of
    the toolkit. In that case the safest way to go
    is to check the Dashboard for a 'green' date and
    download the CVS snapshot at that day using the
    "-D date" option of the 'cvs checkout' command.

3) You could use any of the other formats supported
    by the toolkit. For example,

    - MetaImage
    - GIPL
    - VTK


I would suggest you to use MetaImage, since you can reuse
the binary file of your current Analyze data. MetaImage,
as Analyze use a dual-file format, with a header file
with meta-data information, and a binary file with pixel
information.

You can easily create the MetaImage header that will
load the data in the binary Analyze file. This will
prevent duplication of data in your disk.


BTW, you are absolutely right in that there is no
use in trying any segmentation or registration method
until it is clear that data is being read correctly into
memory.



Please let us know if you encounter any problems,



Regads


    Luis




---------------------------
David Nichols wrote:
> I'm having trouble reading analyze images with itk (Version 1.2.0, the
> standard release on the website, compiled with Visual C++ 6.0, running
> Windows XP).  The program below seems as if it should simply copy the
> input file to the output file, but this doesn't happen.  With the
> program below, if I feed it an Analyze file with 16-bit input the
> output is byte-swapped.  If I change the data type to float (using
> typedef float PixelType;) and provide as input a 32 bit floating point
> set of images the output voxels are all zero.  I can read both of the
> input files with MRIcro, so they seem to be correct.  Does anyone have
> any ideas how to fix this?  Alternatively, is there another way to
> read in 3D data?
> 
> I'd like to register two data sets, but I'd have no confidence in the
> results if I have no confidence that the image data is being read
> correctly.  My initial attempt (using the "Hello world registration"
> from the users guide and changing the dimension from 2 to 3) was
> unimpressive, terminating after 14 iterations with an optimized value
> of about 1.0e6 and producing an output image (the transformed moving
> image) looked like hash.
> 
> Thanks for any advice,
> 
> David Nichols
> Source Signal Imaging
> dnichols at sourcesignal . com
> 
> ============================================================
> 
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkImage.h"
> 
> // Define input image characteristics
> typedef short int PixelType;
> const unsigned int Dimension = 3;
> typedef itk::Image< PixelType, Dimension> ImageType;
> typedef itk::ImageFileReader< ImageType > ReaderType;
> typedef itk::ImageFileWriter< ImageType > WriterType;
> 
> int
> main(int argc, char *argv[])
> {
>  if( argc < 3 ){
>    std::cerr << "Usage : TestReadWriteAnalyze InFile OutFile\n";
>    return( -2 );
>  }
>  // Instantiate reader and writer
>  ReaderType::Pointer reader = ReaderType::New();
>  WriterType::Pointer writer = WriterType::New();
>  // Hook up file names
>  reader->SetFileName( argv[1]);
>  writer->SetFileName( argv[2]);
>  // Connect reader and writer
>  writer->SetInput( reader->GetOutput() );
>  // Ready to roll
>  try {
>    writer->Update();
>  } catch( itk::ExceptionObject &err ){
>    std::cerr << "Exception object caught!" << std::endl;
>    std::cerr << err << std::endl;
>    return( -1 );
>  }
>  return( 1 );
> }
> 
> 
> 
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk . org
> http://www . itk . org/mailman/listinfo/insight-users
>