Hi,
That's a big variability. If you want to use the FSL pipeline, what I would do is:
tbss_1_preproc *.nii.gz
tbss_2_reg -n
tbss_3_postreg -S
Here, I would inspect carefully the all_FA data, to see if the alignment is good, and if it's good:
tbss_4_prestats 0.2 (or a lower value, probably 0.15)
Another option you have is to proceed with pipeline using a combination of FSL and DTI-TK.
Best regards,
Manuel
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