[Insight-developers] *.nii Endianness

[Matt McCormick]

Hi Kevin,

Thanks for the report.  I have created an issue [1] in the issue
tracker to keep track of the issue.

Thanks,
Matt

[1] https://issues.itk.org/jira/browse/ITK-3165

On Tue, Jul 2, 2013 at 5:53 PM, Kevin H. Hobbs <hobbsk at ohio.edu> wrote:
> I'm working on a set of files from ADNI with the extension ".nii".
>
> I don't really know the differences between NIFTI and Analyze formats.
>
> The values in the images differ when I read them with ITK or Paraview
> from the values I get when I read them with Freesurfer or nifti_tool.
>
> I believe this is an endianness issue and I believe that ITK is ignoring
> the endianness of the data.
>
> My machine runs Fedora 17 on x86_64 and I use ITK from a nightly
> dashboard build.
>
> When I read a particular image of pixel type short, with freesurfer or
> nifti_tool I see values in { 20, 21 }.
>
> When I read that same image in ITK or ParaView I see values in { 5120,
> 5376 }.
>
> octave:13> disp(dec2hex ({20,5120,21,5376}))
> 0014
> 1400
> 0015
> 1500
>
> I looked at the file with hexdump and in the data part I see 0014 and
> 0015 which are bigendian 20 and 21.
>
> I asked google about nifti endianness and the nifti header :
>
> http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields
>
> Endianness of the file is determined by looking at dim[0].
>
> The dim field is an array of eight shorts beginning at offset 40.
>
> dim[0] holds the dimension of the image and is restricted to integer
> values from 1 to 7.
>
> dim[1] to dim[7] hold the number of pixels along each dimension.
>
> According to hexdump the 3 dimensional image has "00 03" at byte offset
> 40 so it must have been written on a bigendian machine.
>
> In my ITK reader I have:
>
>   // Reader
>   typedef itk::ImageFileReader< SImageType >  ReaderType;
>   ReaderType::Pointer reader = ReaderType::New();
>   reader->SetFileName( in_file );
>   reader->Update();
>   std::cout
>     << "Read by : "
>     << reader->GetImageIO()->GetNameOfClass() << std::endl;
>   std::cout
>     << "Byte order is : "
>     << reader->GetImageIO()->GetByteOrderAsString(
>       reader->GetImageIO()->GetByteOrder() ) << std::endl;
>
>
> and I get :
>
> Read by : NiftiImageIO
> Byte order is : OrderNotApplicable
>
> ITK correctly interprets the bigendian dimensions "00a6 0100 0100" as
> "166 256 256" instead of the rather strangely shaped little endian
> interpretation "42496 1 1".
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-developers
>