Hi pt, replying to your questions and suggestions:

1) The output of 3dinfo -history $dtipath/SPN01_CMH_0007_01/MASK.nii.gz is simply "NA".
Did you ask me to run this because perhaps we could see how MASK.nii.gz was created? I'll double check with the other researcher who I believe created them. However, I confirm that each binary mask overlays perfectly with each subjects b0 volume (I've checked several subjects to be sure).

2) Re how the mapping/alignment was done: everything was with freesurfer commands. No AFNI tools although I didn't look into that yet. You mentioned that you normally use the the standard aparc+aseg and aparc+aseg2009 ROIs. Could you describe how you would align that into diffusion space? I assume I could just follow those steps for our T1 parcellation.

3) Perhaps this is informative: I have attached 2 screenshots, each showing the overlay with parc5002dwi.nii.gz (the -netrois file). One is in diffusion space and the other is in T1 space. You can see that the first is a perfect match, which makes me *feel* that parc5002dwi.nii.gz was aligned correctly. I have checked this for multiple subjects.

4) Ok, I re-ran 3dinfo with the correct paths this time:

3dinfo \
-obliquity \
-same_grid \
-n4 \
-ad3 \
-prefix \
$dtipath/SPN01_CMH_0007_01/afni/DWUncert+orig. \
$dtipath/SPN01_CMH_0007_01/mri/parc5002dwi.nii.gz \
$dtipath/SPN01_CMH_0007_01/MASK.nii.gz \
$dtipath/SPN01_CMH_0007_01/afni/3dDWItoDT_DT*

And this is the output:
0.000 1 128 128 66 6 2.000000 2.000000 2.000000 DWUncert
0.000 1 128 128 66 1 2.000000 2.000000 2.000000 parc5002dwi.nii.gz
0.000 1 128 128 66 1 2.000000 2.000000 2.000000 MASK.nii.gz
0.000 1 128 128 66 6 2.000000 2.000000 2.000000 3dDWItoDT_DT.nii.gz


Thank you again for your feedback on this!



Edited 1 time(s). Last edit at 10/26/2020 03:10PM by eji.