I got a question for FA display. I run recon-all without error, also no error with dt_recon, mri_vol2vol. I manually checked WM on T1 before displayed FA. Comparing with normal FA display, my FA was out of brain skull. What could the possible problem be during the process? Anyone can help. Thanks in advance !

Here attached the manual checking and FA display (comparing with normal FA)

Best, 

Qi