Hi Manu,
Thanks for your reply!
Yes, I checked the T1-weighted images too, and they were looked fine for me. The picture I attached in this reply shows the images. On the top are the T1-weighted images and the corresponding FA images are below.
I registered the FA image to the original T1 image rather than the BET-calculated T1 image. Is there any chance that the problem was from this?
Best wishes,
Charlie
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