fScan Reference Manual, Chapter 2 (CmdLineOptions): run
-run mode [flag] string
With no arguments, this command just forces everything before it in the command line to be processed before processing other options. A colon (surrounded by blank space) is a shorthand equivalent to the -run command with no arguments. It simply forces execution of all command options preceding it.
With arguments, this loads interactive command strings.
fscan infile -e + 100 -e x 4 -D # add and multiply together (one result window) fscan infile -e + 100 : -e x 4 -D # add and multiply separately (show both results) fscan infile -run "3C4d" -D # load data, switch to 3-plane view and reduce intensity fscan infile -run 2 myview -D # load data and run interactive commands in file "myview" fscan infile -run 3 display 3 -D # load data and run icon 3 from taskbar 'Display' fscan -run 5 run_fslmc infile 9 -v 0 # run the shell script as: "csh run_fslmc INFILE 9"
RUN is a command-line command designed for running sequences of interactive fScan commands.
OPTIONS is a command-line command designed for running sequences of command-line commands.
The 'G' interactive command is designed to run sequences of command-line commands interactively.
Combining and embedding RUN, OPTIONS, and 'G' commands provides a lot of programming flexibility, but can be a bit confusing.
When in doubt, insert ':' (or '-run') into command-line sequences to group sub-sequences into separate processing stages.