This function calls fsl_anat's help
fsl_anat.help()Prints help output and returns output as character vector
if (have.fsl()){
fsl_anat.help()
}
#> Usage: fsl_anat [options] -i <structural image> fsl_anat [options] -d <existing anat directory> Arguments (You may specify one or more of): -i <strucural image> filename of input image (for one image only) -d <anat dir> directory name for existing .anat directory where this script will be run in place -o <output directory> basename of directory for output (default is input image basename followed by .anat) --clobber if .anat directory exist (as specified by -o or default from -i) then delete it and make a new one --strongbias used for images with very strong bias fields --weakbias used for images with smoother, more typical, bias fields (default setting) --noreorient turn off step that does reorientation 2 standard (fslreorient2std) --nocrop turn off step that does automated cropping (robustfov) --nobias turn off steps that do bias field correction (via FAST) --noreg turn off steps that do registration to standard (FLIRT and FNIRT) --nononlinreg turn off step that does non-linear registration (FNIRT) --noseg turn off step that does tissue-type segmentation (FAST) --nosubcortseg turn off step that does sub-cortical segmentation (FIRST) -s <value> specify the value for bias field smoothing (the -l option in FAST) -t <type> specify the type of image (choose one of T1 T2 PD - default is T1) --nosearch specify that linear registration uses the -nosearch option (FLIRT) --betfparam specify f parameter for BET (only used if not running non-linear reg and also wanting brain extraction done) --nocleanup do not remove intermediate files