[Insight-users] VectorImage Orientation from NRRD

[Karthik Krishnan]

Dan, Gordon:

As you've already realized Dan, itk::VectorImage provides no more (and 
no less)
support for direction cosines than itk::Image. They simply ignore it and 
do not,
unlike itk::OrientedImage, take it into account when translating indices 
into
world coordinates, or use it when computing derivatives on images.

NRRD, I believe, allows for encoding both the patient coordinate system
(represented by space_origin and space_directions) and additional
coordinate systems pertinent to DWI images (gradient coil's directions).
Whatever direction cosines it will set on itk::Image or itk::VectorImage are
ignored.

In retrospect, I mistakenly derived VectorImage from ImageBase, rather
than OrientedImage, but both classes came out the same year, when
OrientedImage was still in its infancy with a CVS log stating
"It may be removed be before the next release".

As a solution, the VectorImage class could quite easily be made to
take into account of the direction cosines exactly as OrientedImage does,
by just copying the methods over from OrientedImage. Perhaps that
could be on the list of things ToDo whenever the next lengthy
discussion on Orientation comes up in ITK. I think we have one
every month. :)

Thanks

-- 
Karthik Krishnan
R & D Engineer,
Kitware Inc,
Ph:  518 371 3971 x119
Fax: 518 371 3971


Daniel Betz wrote:
> Hello
>
>   
>> Daniel, Are you saying (at the end of your message) that because  
>> you're using VectorImage, you don't have access to the direction  
>> cosine and m_IndexToPhysicalPoint?
>>     
>
> No. I ever have access to direction; in itk::Image, itk::VectorImage
> and itk::OrientedImage. That is because all of them inherit from
> itk::ImageBase and there is the field m_Direction declared (and also
> m_Origin and m_Spacing). I can access them with the appropriate
> Get/Set methodes.
> You said "its the job of the (unit-length) direction cosines to
> indicate how the samples are arranged along the axes" and I just
> wanted to point out that its true for the itk::OrientedImage. There
> does the SetDirection methode the following:
> <octave>
> o>> m_IndexToPhysicalPoint = m_Direction * diag(m_Spacing)
> </octave>
> So the TransformIndexToPhysicalPoint Methode of itk::OrientedImage
> can do 
> <octave>
> o>> point = m_Origin + sum( [
> o>             m_IndexToPhysicalPoint(1,:) * index(1) ;
> o>             m_IndexToPhysicalPoint(2,:) * index(2) ;
> o>             m_IndexToPhysicalPoint(3,:) * index(3) ] )
> </octave>
> And for my data I would get
> <octave>
> o>> m_Origin = [125 124.1 79.3];
> o>> m_Direction = diag([-1 -1 -1]);
> o>> m_Spacing = [0.9375 0.9375 3];
> o>> m_IndexToPhysicalPoint = m_Direction * diag(m_Spacing);
> o>> index = [ 134 112 11 ];
> o>> point = m_Origin + sum( [
> o>             m_IndexToPhysicalPoint(1,:) * index(1) ;
> o>             m_IndexToPhysicalPoint(2,:) * index(2) ;
> o>             m_IndexToPhysicalPoint(3,:) * index(3) ] )
> point =
>
>    -0.62500   19.10000   46.30000
> </octave>
> My desired RAS coordinates for IJK:(134 112 11).
>
> Enough dreaming; today the implementation of TransformIndexToPhysicalPoint()
> in itk::Image and itk::VectorImage will simply ignore direction and it will
> need some time until they has the same capabilities like itk::OrientedImage.
>
> In the mean time ITK should load the NRRD files like the user would
> expect it. Correctly. Any switch around of the signes should be removed.
>
> If it is really desired to restrict the unoriented itk::Image to LPS
> the only consequent solution would be to load only LPS oriented files
> and to reject the rest.
>
> To store the original "space" field in the MetaDataDictionary would make
> it possible to go back into the right space, but it still would result
> in ugly code.
>
> Regards
> Daniel Betz
>   
> ------------------------------------------------------------------------
>
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