To execute the shell script @DDmb_analyze, it is enough to 'cd' to the directory containing the script and run it: cd howto/ht02_DDmb ./@DDmb_analyze For more information on running a shell script, see ht01_ARzs: Unix help, based on the script from the first HowTo. To learn the commands in the script, it is recommended to enter each command by hand (typing them in, exactly as they appear in the script). The user can do this while reading the AFNI howto and Unix help documents. After each command is entered, the user then has the chance to evaluate the results of that command. Try using the 'ls' (or 'ls -l') command to see which files and directories get created. Try using the 'afni' command to view newly created AFNI datasets.