Hi pt, replying a couple weeks later.

I confirm that with the test subject, there were also 318 GM rois and no memory issues. We recently increased our memory. Further, I've been meaning to try fat_proc_map_to_dti but haven't yet.

In the meantime, I ran 3dInfo on all subjects to check whether the datasets are on the same grid within-subject. Most of them are, as in the previous subject I showed you. However, below are two examples of where things appear to be mismatched:

Subject A:
3dinfo \
> -obliquity \
> -same_grid \
> -n4 \
> -ad3 \
> -prefix \
> $dtipath/SPN01_MRC_0023_01/afni/DWUncert+orig. \
> $dtipath/SPN01_MRC_0023_01/mri/parc5002dwi.nii.gz \
> $dtipath/SPN01_MRC_0023_01/MASK.nii.gz \
> $dtipath/SPN01_MRC_0023_01/afni/3dDWItoDT_DT*
0.000 0 128 135 81 6 2.000000 2.000000 2.000000 DWUncert
6.600 0 128 128 66 1 2.000000 2.000000 2.000000 parc5002dwi.nii.gz
6.600 0 128 128 66 1 2.000000 2.000000 2.000000 MASK.nii.gz
0.000 1 128 135 81 6 2.000000 2.000000 2.000000 3dDWItoDT_DT.nii.gz

Subject B:
3dinfo \
> -obliquity \
> -same_grid \
> -n4 \
> -ad3 \
> -prefix \
> $dtipath/SPN01_MRP_0099_01/afni/DWUncert+orig. \
> $dtipath/SPN01_MRP_0099_01/mri/parc5002dwi.nii.gz \
> $dtipath/SPN01_MRP_0099_01/MASK.nii.gz \
> $dtipath/SPN01_MRP_0099_01/afni/3dDWItoDT_DT*
0.000 0 132 143 100 6 2.000000 2.000000 2.000000 DWUncert
14.750 0 128 128 66 1 2.000000 2.000000 2.000000 parc5002dwi.nii.gz
14.750 0 128 128 66 1 2.000000 2.000000 2.000000 MASK.nii.gz
0.000 1 132 143 100 6 2.000000 2.000000 2.000000 3dDWItoDT_DT.nii.gz

I know the first column refers to degrees from plumb, but I don't understand what plumb is and if it should ideally always be 0. Further, I assume the second column (same_grid) should contain all 1's in order to be used for 3dTrackID? And finally, what about the differences in the other columns?

Thank you.
Ellen