Brain Imaging & Analysis Center

usage:
-run mode [flag] string
-run
:

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.

MODE:

• 1 - interpret STRING as a sequence of interactive commands (default). This sets peekstr to STRING.
• 2 - run contents of file STRING as a sequence of interactive commands
• 3 - STRING is the name of a menu; ITEM is the number of an item within that menu (1=first). If STRING=“funckey”, ITEM is Funckey number. The menu item is run as though it had been selected interactively. Multiple pairs of [MENUNAME ITEM] can be combined in the same '-run 3' command.
• 4 - set contents of file STRING to run when fScan terminates (sets quitstr)
• 5 - run STRING and following arguments as an EXEC command (like interactive cmd: 'STRING',flag E)
• 6 - run contents of file STRING as a sequence of fScan command-line commands
• 7 - run STRING as a sequence of fScan command-line commands

Examples:

  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"

Note:
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.

See Also:
EXEC, OPTIONS, GO

fScan Home, fScan Manual, CmdLineOptions, Manual Help