Hi Paul,

I am sorry for raising this topic again. I know you might not be interested in the old trk.

However, I can not abandon it for some historical reasons in the laboratory :(

I had met a difficulty in opening .trk data from 3dTrackID using matlab. The problem was solved by simply run "spline_filter", another command in the diffusion toolkit, on the trk output from 3dTrackID. And the new .trk data can be accessed correctly.

One interesting thing is the "voxel_order" field.
All my DTI images were in the order of RAI-(or LPS+). And I assume that the trk after tracking on those DTI images should be in the order of RAI-(or LPS+).
The field "voxel_order" read from the trk output was "RAI". (I expect this should be "LPS" according to the trackvis tradition)
And when I open the trk file in trackvis, the tracks looks fine but the FA volume where the tracks was calculated from was totally upside-down, anterior-posterior fliped, and might also left-right flipped.

I also use the dti_tracker, a tracking tool in the diffusion toolkit, to do tracking on FA and tensor images from fatcat. The voxel_order is correct. The trackvis display the information as "LPS->LPS". The FA volume also in right orientation in the trackvis. The matlab also read the information correctly as "LPS"

I feel that the "voxel_order" information set in the trk from 3dTrackID might be in the afni fashion. However, the trackvis use an opposite way to define order.

What's your opinion? If this is true, please help fix this issue. If not, please give me a feedback so I can optimize my pipeline.

I know I can fix this problem by tracking using DTK. However, the 3dTrackID gave me the best tracking results. I hope to solve the most of thing within afni+fatcat suite.

Thanks very much!

Best,
Lz