Hi Wayne,
I think the new release of MITK will support the trackvis file format,
at least if you perform the tracking using the MiniApp command line tool.
But to include the geometry of the image in the output file will only
work for the miniApp, not the GUI application. In the miniApp it is
possible to directly associate the image with the tractogram, which is
in general not possible in the GUI. The new release of MitkDiffusion
will be available soon and hopefully also the MiniApps.
Cheers,
Peter
On 04/11/2014 10:19 PM, Wayne Su wrote:
Re: Save Fiber bundle TrackVis uses LPS coordinate system. But the
fiber bundle saved by MITK uses RAS coordinate system. I managed to
edit the dimension of track file, and translate x and y values in the
track file. Finally I got aligned track and DWI in TrackVis program.
If I’m correct, I suggest to save TrackVis track file in LAS instead
RAS coordinate system. And use the full dimension of upsampled DWI in
1x1x1 resolution, or maybe native DWI space. All this needs to modify
MITK source code.
Wayne
On 14-04-11 8:50 AM, "Wayne Su" <[email protected]> wrote:
Hi Christian,
Thank you for the reply. In the MITK-DT, the fiber bundle aligns
well with T1 and DWI. What I’m trying is to load them into
TrackVis. Because the dimension of the fiber bundle is no longer
same as the one from DWI, they don’t align in TrackVis. I’m
wondering whether there is any option to use the dimension of DWI
(maybe the upsampled DWI with 1x1x1 resolution) to save fiber
bundle. I know there are two ways. One solution is to crop DWI to
match fiber bundle. Another way is to change the dimension of
fiber bundle (I’m not familiar with this part). I appreciate any
input on this case.
Thanks,
Wayne
On 14-04-11 12:56 AM, "Weber, Christian(1)"
<[email protected]> wrote:
Hi Wyane,
the fiber bundles are allways in the space of DWI since they
are derived from it.
Since DWI and T1/T2 often do not match you need to register
them, currently the easiest way doing this with GUI is
(AFAIK ):
Extract B0 image from the DWI and then register the T1 to this
B0 image,
using e.g. the Point-Based registration.
Best,
Christian
*From:* Wayne Su [mailto:[email protected]]
*Sent:* Donnerstag, 10. April 2014 20:10
*To:* [email protected]
*Subject:* [mitk-users] Save Fiber bundle
Hello experts,
Is there a way to save diffusion fiber bundle onto T1
structural space or DWI space, i.e. the dimension of the fiber
bundle is the same as the one from T1 or DWI? Currently, it
saves as reduced dimension with 1mmx1mmx1mm spacing. I tried
to load the track file into TrackVis along with T1 image. But
the locations of them don’t match.
Thanks,
Wayne
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German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung
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