Dear AFNI people,

I've been playing around with some DTI data and found this preprocessing pipeline from a blog by Peter Molfese. I have run the following steps:

Correct Eddy Distortions

3dAllineate -base 'dwi+orig.HEAD[0]' -input 'dwi+orig.HEAD' \
-prefix dwi_al -cost mutualinfo -verb -EPI

Step 2: Fit Tensors using a nonlinear fitting

3dDWItoDT -prefix tensors.nii.gz -automask \
-reweight -verbose 100 -eigs afni.bvecs.txt dwi_al+orig

Step 3: Visualize DTI Data in AFNI

3dcalc -prefix DTIout -a 'tensors.nii.gz[9..11]' -b 'tensors.nii.gz[18]' -expr 'b*STEP(b-0.25)*255*ABS(a)'
3dThreetoRGB -prefix DTIColorMap -anat 'DTIout+orig.[0]' 'DTIout+orig.[1]' 'DTIout+orig.[2]'
afni

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My questions are the following:
-I would like to perform probabilistic tractography, but can it only be done between certain points or for the whole brain?
-Also, after running the scripts above, is it convenient to warp the images to MNI if I want to select some ROIs to run tractography for group comparisons, just like fMRI? and how would I warp these images?
-Also, is it convenient to run 3dDWUncert first and then 3dTrackID -mode PROB?
I am new to this so any suggestions on how to run the analysis would be extremely helpul.

Thanks