Hi Peter,
after a few full days of testing, I found the "issue". In fact, there is no
real issue. As was explained earlier, MITK works in LPS. However, other
tools work in RAS. For example, the tck file format is saved with regards
to the affine from the header of the nifti file that was used to do the
tracking. The only thing I found out is that our colleague that coded tck
support in Mitk had already added a *-1 on the X and Y coordinates, so that
they fit with the volumes. Without knowing it, he was already doing the RAS
-> LPS flip.
The only question that remains, and that probably cannot be answered is:
what do we do with VTK files? If they were created with a tool compatible
with Mitk (or ITK/VTK), they'll be in LPS, so everything will load fine.
However, if they were created by a tool working only with Niftis, and using
the RAS convention, they'll load incorrectly. Sadly, there's no easy way to
detect and correct that automatically.
Thanks everyone for your time!
--
Jean-Christophe
2015-04-23 3:46 GMT-04:00 Peter Neher <[email protected]>:
> Hi JC,
>
> the fibers in MITK are always represented as points in physical space
> without any transform. We simply hand the vtkPolydata, which contains the
> fiber points in world coordinates, to the mapper. No additional transform
> is applied. When saving fibers in vtk/vtp format, a possible transform is
> not preserved anyway. The format does not support that directly as far as I
> know.
>
> Peter
>
>
>
> On 22.04.2015 21:00, Jean-Christophe Houde wrote:
>
> 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 <[email protected]>:
>
>> 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:[email protected]]
>> *Gesendet:* Mittwoch, 22. April 2015 17:07
>> *An:* [email protected]
>> *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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