Hi Manu,
I know that there are sometimes issues with different coordinate system.
E.g. Slicer 3D and MITK are not using the same system. You can simply
mirror the fiber tracking result using MITK Diffusion (Fiber Processing
view). Or if you save the fiber file as .trk file (TrackVis format), the
fibers are mirrored automatically. The 2013.09 version of MITK Diffusion
supports this .trk format.
Peter
On 10/15/2013 03:17 PM, Emmanuel Caruyer wrote:
Thanks, Peter!
I am using the Linux binaries of mitk-diffusion, from the MITK 2013.09
Release. When I open a Nifti LPS image in MITK, and have a look at its
properties (via the "details..." option in the context menu), I see
that the matrix has no longer negative values.
So, taking back the example I gave in my previous email, if the Nifti
affine matrix is as follows:
-2.0 0.0 0.0 130.626465
0.0 -2.0 0.0 121.871460
0.0 0.0 2.0 -75.497993
0.0 0.0 0.0 1.000000
then the matrix and offset in MITK appear like
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 2.0
and -130.626, -121.871, -75.498
So when I get the output of fiber tracking as a vtk file, in order to
match real-world coordinates of the MITK output, and real-world
coordinates of my Nifti image, I basically have to invert x and y axes
in this example. Is this a normal behavior?
Thanks again for your help!
Manu.
2013/10/15 Neher, Peter <[email protected]
<mailto:[email protected]>>
Hi Manu,
the tracks are stored in world coordinates, so no additional
transformation is applied.
Cheers,
Peter
*Von:*Emmanuel Caruyer [mailto:[email protected]
<mailto:[email protected]>]
*Gesendet:* Freitag, 11. Oktober 2013 18:09
*An:* [email protected]
<mailto:[email protected]>
*Betreff:* [mitk-users] Fiber tractography coordinate system
Hi all,
I have a series of DWIs in Nifti with bval/bvec. Images are LPS:
indeed, the affine matrix is:
-2.0 0.0 0.0 130.626465
0.0 -2.0 0.0 121.871460
0.0 0.0 2.0 -75.497993
0.0 0.0 0.0 1.000000
The Gibbs tracking seems to give pretty nice results on this
dataset. Now when I am exporting to vtkPolyData (.vtk), I can't
figure out in which coordinate system the tracks are stored in. It
seems like they are not in the space defined by the
above-mentionned matrix. Is there any documentation on this?
Thanks for your help!
Kind regards,
Manu.
--
Postdoctoral research fellow
Section of Biomedical Image Analysis
University of Pennsylvania
http://www.emmanuelcaruyer.com
--
Postdoctoral research fellow
Section of Biomedical Image Analysis
University of Pennsylvania
http://www.emmanuelcaruyer.com
--
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung
des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: [email protected], Web: www.dkfz.de
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