Hello,
There is a known issue with the FSL 4.1.x version of bet
and certain input options ( including -R -S and -B ). This will be
fixed in the next patch, but to correct this problem before then,
please download:
http://www.fmrib.ox.ac.uk/fsldownloads/patches/bet
and copy it into $FSLDIR/bin/ to install.
Many regards
Matthew
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