Brain Imaging & Analysis Center

There are two different ways to specify processing commands in fScan. These are Command-lines and Command-keys. In general, command-lines are long text strings that can specify a complex series of processing options, whereas command-keys are simpler text strings that specify a single operation. Internally, the main difference is that in command-lines multiple oprerations are parsed together and then executed all at once, while in command-keys each operation is parsed and executed separately. Originally, command lines were entered when fScan was started and command-keys were used to control interactive options. This distinction is no longer strictly true, however, because command-lines can be entered interactively and command-keys can be specified on fScan's startup command line.

The syntax for command-lines has the general form:

      datasetname1 datasetname2 ...  -cmd1 cmd1args -cmd2 cmd2args ...

where the processing commands (-CMD1, -CMD2, etc.) are indicated by their initial '-' character.

The syntax for command-keys has the general form:

      arg1,arg2,...,argN KEY

where KEY is a single letter or control character (e.g. !,@,#,$,?). The optional preceding arguments are usually numbers, but they can also be character strings if they are enclosed in quotes (“). The command is executed as soon as the final <KEY> is read.

An example command-line string is:

mrdata -average -ref 24 24 names text rest skip 4s -ttest text rest -stability

This line would process the fMRI data set MRDATA, performing spatial smoothing (”-average“), specifying the task timing (alternating 24 sec blocks named “text” and “rest”, with 4 sec hemodynamic delay), generating a t-value statistical map (“text” blocks minus “rest” blocks), and plotting head motion and mean image intensity (”-stability“). The 3 image processing operations (averaging, t-test, and stability calculations) will all be performed during a single pass through the data set.

An example command-key is:

Command line options can be joined together, up to a point.

Non-processing set-up options:

"blocks", "group", "header", "input", "list", "roi",
"timebase", "verbose", "writeover", "menu", "history",
"cpus", "wait", "options",

Display options:

"display", "adapt", "overlay", "paint", "plot",

Filtering options:

"mask", "reslice", "images", "lowfreq", "fft",
"despike", "normalize", "average", "convolve",
"regress filter","subset", "join", "output",

Statistical processing:

"correlate", "phase", "regress map"                     - voxel-wise
"mean", "ttest", "variance", "stability"        - image-wise

Surface processing:

"surface",
      "create",
      "new", "window",
      "paint", "paintall", "nocolor", "newpaint",
      "plane", "sphere", "corner", "stereo", "buffer",
      "dynamic","animate", "merge", "output", "functional",
      "draw", "align", "volume", "append", "nofast", "grow"

Arithmetic and other functions:

"expression",
      "-", "+", "x", "/", "min", "max", "gt",  "lt",
      "and", "or", "sqrt", "loc",  "dilate", "erode", "smooth", "flood",
      "boundary", "grow", "thin", "normalize",  "adjust", "peak",
      "gradient", "volmax", "volmin", "overlap", "expand",
      "shrink",  "neighbors", "roimask", "rotate", "flip",
      "convert"

See Also:
fScan Home, fScan Manual, Topics, Manual Help