?I just tested it using the current MITK master and nibabel ?2.1.0. Everything
works fine when either saving directly as .trk or using
MitkFileFormatConverter. I simply used "nib.trackvis.read(filename)".
What version of nibabel and MITK are you using?
As for your alignment issues, I did not test mrview because MITK can not save
.tck files. I tried freeview, but there the fibers did not display at all,
while throwing no error. I am currently downloading trackvis (waiting for the
registration email) for further testing.
Peter
?
________________________________
Von: Neher, Peter
Gesendet: Mittwoch, 5. April 2017 14:52
An: Alexandre Dupoint; mitk-users@lists.sourceforge.net
Betreff: AW: [mitk-users] Convert tractography tracts to trk / tck formats
?Hi Alexandre,
simply saving the results as .trk files should work. I did not encounter the
nibabel issue with a missing voxel_to_ras matrix yet, but I will look into it.
Could you send me a sample trk file that I can use to reproduce the error?
Cheers,
peter
?
________________________________
Von: Alexandre Dupoint <alexandre.dupo...@mail.com>
Gesendet: Mittwoch, 5. April 2017 14:12
An: mitk-users@lists.sourceforge.net
Betreff: [mitk-users] Convert tractography tracts to trk / tck formats
Hi
I have tractograms (.fib) generated with MITK Gibbs Tracking that I would like
to convert to TRK (or TCK) to be able to look at them with other tools.
I have tried many things but I haven't been able to generate TRK files where
tracks align with the associated diffusion data when opening with tools like
Freeview (FreeSurfer), mrview (MRtrix) or TrackVis
Some of the things I tried:
- converting with TractConverter
(https://github.com/MarcCote/tractconverter) using the diffusion data as
spatial reference
- converting to TRK with MitkFileFormatConverter.sh: when loading with
nibabel it complains about a missing voxel_to_ras matrix
- converting the .fib to a parsable text file with Paraview, parsing this
text file to generate a Nibabel tractogram and associating it with affine
matrix of the diffusion data to create a TRK file
I also tried to apply transformations on the streamlines and tried to edit
header informations like RAS to LPS but I don't have a good enough
understanding of the subject to get the tracks aligned with diffusion.
I hope someone can give me a hint. Thank you.
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