**fScan Reference Manual, Chapter 1 (Topics): processing**

===== processing -- =====

There are two different ways to specify processing commands in fScan.
These are [[jvs:fscan:manual:chapter1:cmdlins|Command-lines]] and 
[[jvs:fscan:manual:chapter1:cmdkeys|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:**\\
[[jvs:fscan|fScan Home]], 
[[jvs:fscan:manual|fScan Manual]], 
[[jvs:fscan:manual:chapter1|Topics]], 
[[jvs:fscan:manual:help|Manual Help]]