Hello Freesurfer experts, I have a question regarding the use of the -T2 and -FLAIR flags in freesurfer. I have 2 scans: 1 whole brain MPRAGE and 1 partial brain FLAIR (bottom of cerebellum/brainstem gets cut off on some subjects). I wanted to see if freesurfer would still be able to run correctly if my FLAIR image is aligned, BUT DOES NOT COVER the exact same amount of the brain as my MPRAGE? I checked with autorecon1 and the mask seemed to cover the whole brain, however I am not sure if there are any subsequent steps that might not behave properly such lesion detection, surface creation etc.
Thanks, Ajay
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