This function calls bet's help
fslbet.help(betcmd = c("bet2", "bet"))(character) Get help for bet or bet2 function
Prints help output and returns output as character vector
if (have.fsl()){
fslbet.help()
fslbet.help("bet")
}
#>
#> Usage: bet <input> <output> [options]Main bet2 options: -o generate brain surface outline overlaid onto original image -m generate binary brain mask -s generate approximate skull image -n don't generate segmented brain image output -f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates -g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top -r <r> head radius (mm not voxels); initial surface sphere is set to half of this -c <x y z> centre-of-gravity (voxels not mm) of initial mesh surface. -t apply thresholding to segmented brain image and mask -e generates brain surface as mesh in .vtk formatVariations on default bet2 functionality (mutually exclusive options): (default) just run bet2 -R robust brain centre estimation (iterates BET several times) -S eye & optic nerve cleanup (can be useful in SIENA - disables -o option) -B bias field & neck cleanup (can be useful in SIENA) -Z improve BET if FOV is very small in Z (by temporarily padding end slices) -F apply to 4D FMRI data (uses -f 0.3 and dilates brain mask slightly) -A run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations) -A2 <T2> as with -A, when also feeding in non-brain-extracted T2 (includes registrations)Miscellaneous options: -v verbose (switch on diagnostic messages) -h display this help, then exits -d debug (don't delete temporary intermediate images)