This first exercise will create a script that applies BET to an image prior to registering it with another image.

1. Editing a text file
   Create a new file called bet_vol using the nano text editor.
   To do this just type (in a terminal):
       nano bet_vol
   Notes:
   • Feel free to use any other text editor that you prefer

2. Making the script
   In this file write a script (one command) which applies BET to a volume called vol and saves the result as vol_brain.
   That is use the same command as you would use in the terminal:
       bet vol vol_brain
   Remember that the first line must be #!/bin/sh

3. Running the script
   Save the script
   Copy the image im1 to vol (with the .nii.gz extensions)
   Remember to make the script executable with:
       chmod a+x bet_vol
   Run the script by typing ./bet_vol (you need the "./" because the current directory (".") may not be in your PATH)

4. Testing the script
   Check that the script wrote out the image vol_brain and that the result is sensible (do a visual check with slices)

5. Commenting the script
   Add a comment to the script that explains what it does.
   A comment is any line (except the first) which starts with #

   If you are stuck you can look at the cheat.