Hi,
(1) open in FSLeyes an MNI template (e.g., FMRIB58_FA_1mm)
(2) go to Settings > Ortho View > Atlas Panel
(3) Select the Atlas and then look in the "Atlas search" tab for your tract of interest
(4) "Check" the tract of interest to add it to your overlay list
(4) Save overlay
(5) Play with the FSLroi command to find a threshold that suits you well
(6) Binarize this as a mask
(7) Run fslmeants -i all_FA.nii.gz -m tract_binarized.nii.gz > tract_FA.txt
Make sure your FA maps are in the same dimension (and space) as the MNI template.
Best,
J
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