It's easy to correct. I also do it when tracking with mrtrix. You can
use the MITK MiniApp MitkFiberProcessing to flip the fibers. Here is an
example with mrtrix:
1. Use streamtrack to create a .tck file
2. use tracks2vtk to convert .tck to .fib (which is vtk)
3. MitkFiberProcessing -i myFibers.fib -p 110 -o myFlippedFibers.fib
the -p option lets you specify the flipping dimension. in this case the
fibers are flipped in x and y but not in z direction (110). so using -p
110 converts from RAS to LPS.
Peter
On 27.04.2015 14:58, Jean-Christophe Houde wrote:
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 <p.ne...@dkfz-heidelberg.de
<mailto:p.ne...@dkfz-heidelberg.de>>:
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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