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fScan Reference Manual, Chapter 2 (CmdLineOptions): Contents

Command Line Options -- Summary List

Quick reference list

A broad range of fScan processing features are controlled by “command-line option” operators. Command-line options can be specified on the fScan command line, as batched commands via Options command files, or interactively via the Go command, Menus, or Taskbars.

For a general description of fScan command-line options and how they compare to interactive key commands see fScan Commands.
See the fScan Programming page for a discussion of how to combine commands to perform more complex functions.

Summary list of command line options (Select individual command names for more information on that option):

Command nameAliasDescription
accumulate-AAccumulate values for calculating means, StDevs, and trial counts
align Auto-align images by optimizing mutual information
ample Generate AMPLE normalized activation maps and stability plots
average-aAverage input voxels in space or time
blocks Specify block condition in 1 cycle
browse Select items from a list
connect Open an external port connection
convolve Convolve images using kernal matrix
correlate-CCalculate temporal correlation coefficient activation maps
cpus-QDistribute processing of large runs across multiple parallel processors
create Create surface reconstructions or paint surfaces from images
delete Delete a data set
design Create and manipulate task design matrix
despike Count and/or remove signal spikes from time course data
detrend Remove slow temporal fluctuations (detrend)
display-DSpecify display options
dmread Read DM format files (pdigms etc)
echo-EEcho command arguments, substituting variable values
execute-XExecute other programs by launching a shell script
expression-ePerform arithmetic expressions on whole data sets
fft-FPerform a fast Fourier transform (FFT)
fithrf Fit a hemodynamic response function to time series data
glm-gGeneral linear model statistics
group-gSelect grouping variable (for -mean -stdev -ttest -accumulate)
header-hOutput file format specifications
history-HAdd file HIST to history
images-IReconstruct images from raw data
if Test some condition before executing commands
input-iSpecify input image codes
join-jJoin conditions COND2 … with COND1
lowfreq Remove slow temporal fluctuations (detrend)
mask-mSpecify binary (byte) mask image for input
mean-MGenerate mean images
movie Generate a time series data set from other data
normalize-NNormalize intensities to a constant mean
options-ORead and execute a file containing fScan commands
output-oWrite a data set to a disk file
phase-PCreate a phase map
physio Analyze physiological waveforms
plot-pPlot data in a graph
raw Save a copy of the input raw data prior to any processing steps
recon Reconstruct images from raw data
reference-rSpecify timing information
reflist Specify image reference codes
regress-RMap temporal fluctuations by condition
reorder-JRearrange the order in which data appears in a data set
reslice-zResample a 3-D volume data set
rfilter Unmodulate temporal fluctuations by condition
rmap Map temporal fluctuations by condition
roi-bprint STDOUT ROI stats
run Force execution of previous command options
set-YSet the value of internal variables
show Show program status or values of data variables
square Clip to square images
stability-dGenerate plots of changes in image position and intensity
stabplots Calculate displacements of center-of-mass
stats Calculate simple mean, stdev, and count statistics
stdev-VGenerate variance images
surface-SSurface data
table-tManipulate tables – lists of text and numbers
ttest-TGenerate activation maps based on t-test comparisons
variance Generate variance images
verbose-vSet program diagnostic and debugging flags
wait-WWait for external events to synchronize data processing
writeover-wWrite flag


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

jvs/fscan/manual/chapter2.1312304965.txt.gz · Last modified: 2014/08/04 16:03 (external edit)