Thanks for sending that info.

The commands in #1 and #2 look fine. Depending on the data, in the 3dDWUncert command having more than 50 iterations might be useful, like having ~300 hundred. The Bootcamp demo uses 50 for speed considerations. It is a question of convergence of the uncertainty distributions (at the cost of speed for more iterations). But that shouldn't be causing the issues here in 3dTrackID.

Re. #3:
The mask looks like a mask, though I can't see it's overlap with the data... What is "3dinfo -history $dtipath/{}/MASK.nii.gz"?

Re. #4:
Interesting, OK. I am not familiar with this process at all with FS; I normally use the aparc+aseg and aparc+aseg2009 ROIs from their outputs. But given the number of steps and mapping, I wonder if the final grid of this dset is mismatched with the others? What did you use for the mapping/alignment process? AFNI tools, and if so, which one(s)? When bringing them to the diffusion space, is the "-master .." dset one of the diffusion ones, so the grid will be correct?

Re. the 3dinfo command:
Well, I was trying to use your file names and paths... but you need to provide the correct name/path for each of your datasets, which appear to be in different places. The paths for 3dDWUncert+orig and 3dDWItoDT_* are not correct, hence the output of NO-DSET for those two items. Can you please run this modified/expanded form, putting in the correct paths for where "[some path]" is written (if you get NO-DSET showing up, then something isn't correct and the path needs to be fixed):

3dinfo \
   -obliquity \
   -same_grid \
   -n4   \
   -ad3 \
   -prefix \
   [some path]/DWUncert+orig.  \
   $dtipath/{}/mri/parc5002dwi.nii.gz  \
   $dtipath/{}/MASK.nii.gz   \
   [some path]/3dDWItoDT_DT*

(though I think the output of even that first command shows that the MASK and parc5002 dsets are on different grids.)

-pt