[mitk-users] Convert tractography tracts to trk / tck formats

[Alexandre Dupoint]

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.

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
mitk-users mailing list
mitk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mitk-users