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I noticed what is likely a very minor bug. The help information for the bet script that wraps bet2 (i.e. run bet with no arguments) claims that the -F option, intended for use with fMRI timeseries, uses a fractional intensity threshold (i.e. -f) of 0.4 when, in actuality, it is using -f 0.3. See line 327 of the bet script. My personal feeling is that -f 0.4 works better (-f 0.3 tends to leave behind the eyeballs), but either way the documentation and the actual script should probably match.