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".
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