Hi Caspar,
it all makes sense. However, that raises another semi-related question: we
are currently coding a loader for the .tck streamlines format. The .tck
format (at least from mrtrix version 0.2) saves the points in world space,
using the underlying image transform as the reference. So, normally, points
are saved as RAS.
When reading the file, we take the file as-is, and put the points in
a vtkPolyData without doing any transform. What is surprising is that, even
though MITK uses a LPS coordinate system, our points (which follow a RAS
coordinate system) are displayed exactly in the correct spot...
Therefore, I'm wondering if there is any additional transform that is done
by the rendering code, or if there is another aspect I didn't take into
account...
Best,
--
Jean-Christophe
2015-04-22 13:25 GMT-04:00 Goch, Caspar Jonas <c.g...@dkfz-heidelberg.de>:
> Hi Jean-Christophe,
>
>
>
> MITK uses ITK for a lot of the image loading and Nifti in particular
> [1,2]. Due to that it shares ITK’s preferred orientation LPS. AFAIK the
> q/sform uses RAS as a standard, so the flip is probably due to ITK
> conversions as you assumed.
>
>
>
> Does this answer your question?
>
>
>
> Best,
>
> Caspar
>
>
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1NiftiImageIO.html
>
> [2] http://www.itk.org/Doxygen/html/classitk_1_1ImageIOBase.html
>
>
>
>
>
> *Von:* Jean-Christophe Houde [mailto:jean.christophe.ho...@gmail.com]
> *Gesendet:* Mittwoch, 22. April 2015 17:07
> *An:* mitk-users@lists.sourceforge.net
> *Betreff:* [mitk-users] Orientation and transforms question
>
>
>
> Hi everyone,
>
>
>
> I would like to have some clarifications on the interpretation of
> orientations and transforms in Mitk. First, what is the preferred
> orientation in MITK? LPS, RAS, or something else?
>
>
>
> Secondly, there always seems to be some modifications applied to the
> affines of my images when I load them. When looking at the affine
> information in the Nifti image available in [1], using fslhd, I get a qform
> of
>
>
>
> qform_code 1
>
> qto_xyz:1 1.000000 -0.000000 0.000000 -125.834106
>
> qto_xyz:2 0.000000 1.000000 -0.000000 -103.860718
>
> qto_xyz:3 0.000000 0.000000 1.000000 -53.192493
>
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>
>
>
> and a sform of
>
>
>
> sform_code 1
>
> sto_xyz:1 1.000000 0.000000 -0.000000 -125.834106
>
> sto_xyz:2 0.000000 1.000000 -0.000000 -103.860718
>
> sto_xyz:3 0.000000 0.000000 1.000000 -53.192493
>
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
>
>
>
> which are exactly the same, save for some -0 switched to 0 and vice-versa.
> Those switches should have no effect, at least to my knowledge.
>
>
>
> However, when loading this image in a software built on Mitk (based on
> release 2014.10), the IndexToWorld transform shown in the details of the
> image is
>
>
>
> IndexToWorldTransform:
>
> Matrix: -1 0 -0
>
> -0 -1 0
>
> 0 0 1
>
> Offset: [125.834, 103.861, -53.1925]
>
>
>
> Clearly, there is a -1 factor on the 2 first rows of the transform (and
> therefore, on the offset as well). I guess it's a transform to go from RAS
> to LPS? If so, is this always applied on Nifti images, or there are some
> specific cases?
>
>
>
> This really has some implications when we want to save, for example, a VTK
> polydata file in a tool outside of Mitk, and the load it inside Mitk.
>
>
>
> Thanks for your time!
>
>
>
> [1] https://dl.dropboxusercontent.com/u/53085014/mitk/t1.nii.gz
>
>
>
> ---
>
> Jean-Christophe Houde, M.Sc.
>
> Research assistant
>
> Sherbrooke Connectivity Imaging Lab
>
> Sherbrooke University
>
>
>
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