Hi paul,
This is a reasonable hypothesis from my observation.
If the voxel order was in "RAI" according to 3dinfo, the "voxel_order" field in the header stored in the .trk output should be "LPS".
I had not try the order of "IPL".
And I am not sure whether it will affect the coordinates stored in .trk data.
If not, I think simply fixed the "voxel_order" stored in .trk data by using the opposite of 3dinfo output will help.
I had tried to use diffusion toolkit (DTK) to do tracking and avoid the problem. However, the DTK performs poorly on a recent dataset from a Philips MRI scanner. The 3dTrackID gave me very good results. That's why I want to construct my pipeline on afni+totose+fatcat as much as possible.
Thanks very much!
Best,
-Lizhuang
