Hi pt, yes we obtained T1, T2 and dwis. I don't think T2 was used in any step of the process and tbh I'm not sure if dwis were dual phase encoded.

On a related note, I now left out 3dWarp -deoblique and then ran 3dInfo to look at the data necessary for 3dTrackID:

3dinfo \
> -is_oblique \
> -obliquity \
> -same_grid \
> -n4 \
> -ad3 \
> -prefix \
> $dtipath/SPN01_MRC_0001_01/afni/DWUncert+orig. \
> $dtipath/SPN01_MRC_0001_01/mri/parc5002dwi.nii.gz \
> $dtipath/SPN01_MRC_0001_01/MASK.nii.gz \
> $dtipath/SPN01_MRC_0001_01/afni/3dDWItoDT_DT*
1 4.159 1 128 128 66 6 2.000000 2.000000 2.000000 DWUncert
1 4.159 1 128 128 66 1 2.000000 2.000000 2.000000 parc5002dwi.nii.gz
1 4.159 1 128 128 66 1 2.000000 2.000000 2.000000 MASK.nii.gz
1 4.159 1 128 128 66 6 2.000000 2.000000 2.000000 3dDWItoDT_DT.nii.gz

At least now everything is on the same grid. Would it then be *ok* that there is obliquity since they all reflect the same degree from plumb? What is the 7th column, which seems to be the only difference? (6 vs 1)