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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