Dear Freesurfer team,

I have done FA quantification in brainstem substructures using two ways and got slightly different results.

First, I used dMRI Data Analysis Processing Stream with the following steps (after brainstem segmentation followed by dt_recon) -
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0)

dt_recon - mri_vol2vol - masking - mri_segstats using FreeSurferColorLUT.txt

In the second approach, I used vol2subfield after brainstem segmentation followed by dt_recon.
 
dt_recon - vol2subfield

Which one is more accurate for FA quantification?

Thanks and Regards,
Puneet

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