Hi,
This stuff is all quite confusing I'm afraid, but I think I know what
is going on.
If you look at the full output of fslhd, you should see that the
qform_name is
Unknown and the qform_code is 0 (the former is a worded description
of the
latter). This indicates that this nifti file *does not contain*
orientation information
(assuming your sform_name is Unknown as well). Hence the fslhd program
guesses the x_orient based on a default qform, which isn't useful I'm
afraid.
The alternative output with fslhd -x only shows you the sform and
qform when
they contain useful information - so maybe you'll find that better.
In general it is dangerous to use nifti files without any orientation
information or
to use Analyze (as it has no intrinsic, standard orientation
information in it).
Internally to most fsl tools, such orientation-less files will be
treated as radiological
where it matters (e.g. in flirt) and things should work fine.
However, to be safer
it is best to encode the information in nifti file if you are sure
which way around the
axes are. You can change the nifti information with fslorient. Note
that you need
to set either the sform or qform code to a non-zero value first, as
otherwise it will
ignore all attempts to include orientation information. You can
check if you have
things correct by using FSLView which will label your axes based on
this info.
I hope this helps make things clearer.
All the best,
Mark
On 29 Nov 2007, at 21:05, Jon Clayden wrote:
> Dear all,
>
> I'm confused about FSL's conventions for dealing with Analyze
> files. It says on the FSL site at <http://www.fmrib.ox.ac.uk/fsl/
> fsl/formats.html> that Analyze files are treated as being in
> radiological convention, i.e. LAS. However, if I convert an Analyze
> file to Nifti using fslchfiletype I get a header indicating that
> the file is *RAS*, as shown below. Moreover, the image data is
> unchanged, rather than being flipped left-to-right as seems to be
> the case with the header.
>
> Can anyone shed any light on why this is?
>
> Cheers,
> Jon
>
>
> $ ls basic*
> basic.hdr.gz basic.img.gz
> $ fslhd basic | grep -a file_type
> file_type ANALYZE-7.5
> $ cp basic.hdr.gz basic2.hdr.gz
> $ cp basic.img.gz basic2.img.gz
> $ ls basic*
> basic.hdr.gz basic.img.gz basic2.hdr.gz basic2.img.gz
> $ fslchfiletype NIFTI_PAIR_GZ basic2
> $ fslhd basic2 | grep xorient
> qform_xorient Left-to-Right
> sform_xorient Unknown
> $ diff basic.img.gz basic2.img.gz
> $
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