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--- jvs:fscan:manual:chapter2:run [2011/12/20 18:48]
voyvodic
+++ jvs:fscan:manual:chapter2:run [2016/07/19 19:23]
voyvodic
@@ Line 2: / Line 2: @@
 ===== Run -- Execute a series of fScan interactive commands =====
 **usage:**\\
- %%-run flag string%%\\
+ %%-run mode [flag] string%%\\
  %%-run%%\\
  %%:%%
@@ Line 10: / Line 10: @@
 With arguments, this loads interactive command strings.
-FLAG:
+MODE:
-  * 1 - interpret STR as a sequence of interactive commands (default). This sets [[jvs:fscan:manual:chapter4:peekstr|peekstr]] to STR.
+  * 1 - interpret STRING as a sequence of interactive commands (default). This sets [[jvs:fscan:manual:chapter4:peekstr|peekstr]] to STRING.
-  * 2 - run contents of file STR as a sequence of interactive commands
+  * 2 - run contents of file STRING as a sequence of interactive commands
-  * 3 - STR 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.
+  * 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 STR to run when fScan terminates (sets [[jvs:fscan:manual:chapter4:quitstr|quitstr]])
+  * 4 - set contents of file STRING to run when fScan terminates (sets [[jvs:fscan:manual:chapter4:quitstr|quitstr]])
-  * 5 - run STR as a synchronous fScan shell command
+  * 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:
 <code>
-  fscan infile -e + 100 : -e x 4 -D           # process image addition and multiplication separately (show both results)
+  fscan infile -e + 100   -e x 4 -D           # add and multiply together (one result window)
-  fscan infile -e + 100   -e x 4 -D           # addition and multiplication will be done 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 set, switch to 3-plane view and reduce intensity
+  fscan infile -run "3C4d" -D                 # load data, switch to 3-plane view and reduce intensity
-  fscan infile -run 1 myview -D               # load data set and run interactive commands in file "myview"
+  fscan infile -run 2 myview -D               # load data and run interactive commands in file "myview"
-</code>
+  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"
+</code>
 **Note:**\\
 RUN is a command-line command designed for running sequences of interactive fScan commands.\\
 [[jvs:fscan:manual:chapter2:options|OPTIONS]] is a command-line command designed for running sequences of command-line commands.\\
 The '[[jvs:fscan:manual:chapter3:winkeys:go|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.
+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:**\\

Brain Imaging & Analysis Center

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