Dear FSL users,
When I try and fnirt my subject brain to MNI152_T1_1mm the result ends up being my subjects brain registering to the skull of MNI152_T1_1mm. Therefore I tried to use the --applyrefmask option in my config file and no difference. I then noticed that the log file has no information on --applyrefmask and was wondering if it's actually doing anything.
Any help would be greatly appreciated.
Dustin
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