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
<c.g...@dkfz-heidelberg.de <mailto: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
<mailto:jean.christophe.ho...@gmail.com>]
*Gesendet:* Mittwoch, 22. April 2015 17:07
*An:* mitk-users@lists.sourceforge.net
<mailto: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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