[mitk-users] Convert tractography tracts to trk / tck formats
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[mitk-users] Convert tractography tracts to trk / tck formats
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From: Alexandre D. <ale...@ma...> - 2017-04-05 12:12:34
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<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div> <div>Hi</div> <div> </div> <div>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.<br/> 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</div> <div> </div> <div>Some of the things I tried:<br/> - converting with TractConverter (https://github.com/MarcCote/tractconverter) using the diffusion data as spatial reference<br/> - converting to TRK with MitkFileFormatConverter.sh: when loading with nibabel it complains about a missing voxel_to_ras matrix<br/> - 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</div> <div> </div> <div>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.</div> <div> </div> <div>I hope someone can give me a hint. Thank you.</div> </div></div></body></html> |
