?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 <[email protected]> Gesendet: Mittwoch, 5. April 2017 14:12 An: [email protected] 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. ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
