The following is the code I used to run bet:
fslvbm_1_bet -N -f 0.6
However, my study consists of a control group and a neurodegenerative group which has atrophy in frontal and temporal lobes. After I run bet, I am looking at the results and it appears that for one patient the program has failed to extract the brain - the slice directory shows no red outlines around the brain.
Wondering if there is a reason why, or if there is a way to circumvent this issue.
Many thanks
Karim
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