[Insight-users] Analyze IO

[Karthik Krishnan]

Thanks for verifying. And please ignore the previous mail.

I don't know if there is a way to specify an origin in Analyse files. 
This might be a limitation of the file format itself.

 From
http://www.mayo.edu/bir/PDF/ANALYZE75.pdf
there seems to be no field to specify the origin. The example provided 
above does not consider it either..

In fact other software tools like SPM adopt their own heuristics:

(From http://www.mrc-cbu.cam.ac.uk/Imaging/Common/analyze_fmt.shtml)

"SPM modifications of the basic analyze format"

The image origin is specified in the Originator field 
(data_history.originator - see Mayo/Analyze site). In the basic format, 
this is meant to be 10 bytes of text. In SPM, this space is used to 
contain three short (two byte) integers. These numbers describe the 
current centre or 'Origin' of the image. Specifically, they give the 
coordinate of the central voxel, in voxels, in X, then Y then Z. For 
example, for images that are aligned to the templates, this Origin field 
would contain the coordinates of the voxel nearest to the midline of the 
Anterior Commisure. Note that if the Origin is set to 0 0 0, then SPM 
routines will assume that the origin is in fact the central voxel of the 
image."

Thanks
Regards
karthik




Gheorghe Postelnicu wrote:

> Actually I manually created the image (using the RawImageIO) and then 
> opted at first for .img extension when I was writing the file.
>
> Here is my code :
>
>
> -----
> template<class T>
> static void
> convert(VolumePars pars)
> {
>
>   // declare types
>
>   typedef T PixelType;
>   typedef typename itk::Image<PixelType,Dimension> ImageType;
>   typedef typename itk::RawImageIO<PixelType,Dimension> ImageIOType;
>   typedef typename itk::ImageFileReader<ImageType> ReaderType;
>
>  
>   typename ReaderType::Pointer reader = ReaderType::New();
>   typename ImageIOType::Pointer rawIO = ImageIOType::New();
>
>
>   rawIO->SetFileDimensionality(3);
>   rawIO->SetOrigin(0, pars.originX);
>   rawIO->SetOrigin(1, pars.originY);
>   rawIO->SetOrigin(2, pars.originZ);
>
>   rawIO->SetDimensions(0, pars.dimX);
>   rawIO->SetDimensions(1, pars.dimY);
>   rawIO->SetDimensions(2, pars.dimZ);
>
>   rawIO->SetSpacing(0, pars.spacingX);
>   rawIO->SetSpacing(1, pars.spacingY);
>   rawIO->SetSpacing(2, pars.spacingZ);
>
>   rawIO->SetByteOrderToLittleEndian();
>
>   reader->SetFileName(pars.inputBuffer.c_str());
>   reader->SetImageIO( rawIO );
>
>   try { reader->Update(); } catch(itk::ExceptionObject& excp)
>     {
>       std::cerr << "Exception caught while reading file " << 
> reader->GetFileName() << std::endl
>         << excp << std::endl;
>       exit(1);
>     }
>
>   std::cout << "done reading RAW image PARAMETERS\n"
>         << "sizes = " << 
> reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl
>         << "origin = " << reader->GetOutput()->GetOrigin() << std::endl
>         << "spacing = " << reader->GetOutput()->GetSpacing()  << 
> std::endl;
>  
>   typedef typename itk::ImageFileWriter<ImageType> WriterType;
>   typename WriterType::Pointer writer = WriterType::New();
>
>   writer->SetFileName(pars.outputFileName.c_str());
>   writer->SetInput(reader->GetOutput());
>   try { writer->Update(); } catch(itk::ExceptionObject& excp)
>     {
>       std::cerr << "Exception caught while writing\n"
>         << excp << std::endl;
>       exit(1);
>     }
>
> }
>
> ------
>
> As you can see, the origin of the image is displayed before the image 
> is saved.
>
> After noticing that I had some placement problems, I wrote another 
> binary which was just loading an image in ITK and displaying the 
> information. When using the .img extension, the origin information was 
> lost.
>
> I looked very briefly in the itkAnalyzeImageIO.cxx file and it appears 
> some origin information is written in some metadata associated with 
> the image. I have seen on the internet some proposal to include 
> orientation information which used the same mechanism.
>
> Thanks,
>
> On 12/9/05, *Karthik Krishnan* <Karthik.Krishnan at kitware.com 
> <mailto:Karthik.Krishnan at kitware.com>> wrote:
>
>     Please let us know what format you converted from ? The bug might be
>     that the origin data was never read in .
>
>     I've written analyse images in ITK before and they seem to retain the
>     origin information.
>
>     I have observed that InsightApplications/ImageViewer does not respect
>     image origins when it reads files. So are you basing your
>     assumptions on
>     images seen using ImageViewer ? If you use any of the several other
>     viewers, you should find that the origin info is recorded.
>
>     thanks
>     karthik
>
>     Gheorghe Postelnicu wrote:
>
>     > Hi,
>     >
>     > I have recently used ITK to convert some files to the Analyze format
>     > and I have noticed that the origin data is lost when writing the
>     > volume file. I haven't gone further than this, but is this normal?
>     >
>     > As far as I am concerned, this is quite annoying when doing
>     registration.
>     >
>     > Thanks,
>     > --
>     > Gheorghe Postelnicu, PhD
>     > MGH, Harvard Medical School
>     >
>     >------------------------------------------------------------------------
>     >
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>     >
>     >
>
>
>
>
> -- 
> Gheorghe Postelnicu, PhD
> MGH, Harvard Medical School
>
>------------------------------------------------------------------------
>
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