I have added a new option to 3dTrackID called "-trk_opp_orient":
-trk_opp_orient :If outputting *.trk files, you can choose to oppositize
the voxel_order parameter for the TRK file (only).
Thus, when inputting AFNI files with orient RAI, the
*.trk file would have voxel_order LPS; this is so that
files can be viewed in some other software, such as DTK.
Please let me know if that works. You might also want to check on resampled data that has other orientations than just RAI (in AFNI-speak).
It is available in the most recent binaries, so you can update your AFNI version to get it. Please let me know if that sorts things out for you using TRK output in DTK.
-pt