fScan Reference Manual, Chapter 1 (Topics): processing
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