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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