Adding Command Line Arguments
  1. Specifying image filenames on the command line
    Take the bet_vol script and modify it so that it applies BET to the image filename passed in as the first command line argument.

    That is, if you type: ./bet_vol im2
    then it should apply BET to the image im2 and save the result as im2_brain

  2. Testing
    Try running the script with im2 as the input.
    Check that the resulting image has the correct name and that the image itself looks right.
    Note: the argument should not include the .nii.gz part of the filename

  3. Passing arguments to BET (Advanced)
    You can pass any additional arguments of the script onto BET (e.g -f 0.4 -g 0.1) using the $@ variable.
    However, as you do not want to repeat the input filename this can be removed from the argument list using shift
    Once the command shift is executed inside a script the first argument $1 is removed and all others shuffle down one number.
      That is, $2 becomes $1, while $3 becomes $2 etc.
    Using shift and $@ pass the extra arguments as following options to the BET command line call.

    Look here for the cheat.