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fScan Reference Manual, Chapter 2 (CmdLineOptions): Contents
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 name | Alias | Description | |
---|---|---|---|
accumulate | -A | Accumulate values for calculating means, StDevs, and trial counts | |
adapt | |||
align | Auto-align images by optimizing mutual information | ||
ample | Generate AMPLE normalized activation maps and stability plots | ||
average | -a | Average input voxels in space or time | |
bandpass | -B | ||
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 | -C | Calculate temporal correlation coefficient activation maps | |
cpus | -Q | Distribute 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 | -D | Specify display options | |
dmread | Read DM format files (pdigms etc) | ||
echo | -E | Echo command arguments, substituting variable values | |
execute | -X | Execute other programs by launching a shell script | |
expression | -e | Perform arithmetic expressions on whole data sets | |
fft | -F | Perform a fast Fourier transform (FFT) | |
fithrf | Fit a hemodynamic response function to time series data | ||
glm | -g | General linear model statistics | |
group | -g | Select grouping variable (for -mean -stdev -ttest -accumulate) | |
header | -h | Output file format specifications | |
help | -? | ||
history | -H | Add file HIST to history | |
images | -I | Reconstruct images from raw data | |
if | Test some condition before executing commands | ||
input | -i | Specify input image codes | |
join | -j | Join conditions COND2 … with COND1 | |
list | -l | ||
lowfreq | Remove slow temporal fluctuations (detrend) | ||
mask | -m | Specify binary (byte) mask image for input | |
meanstdev | |||
mean | -M | Generate mean images | |
menu | -K | ||
movie | Generate a time series data set from other data | ||
normalize | -N | Normalize intensities to a constant mean | |
options | -O | Read and execute a file containing fScan commands | |
output | -o | Write a data set to a disk file | |
overlay | -U | ||
paint | -u | ||
pctsignal | |||
peaks | |||
phase | -P | Create a phase map | |
physio | Analyze physiological waveforms | ||
plot | -p | Plot data in a graph | |
query | -q | ||
raw | Save a copy of the input raw data prior to any processing steps | ||
recon | Reconstruct images from raw data | ||
reference | -r | Specify timing information | |
reflist | Specify image reference codes | ||
regress | -R | Map temporal fluctuations by condition | |
reorder | -J | Rearrange the order in which data appears in a data set | |
reslice | -z | Resample a 3-D volume data set | |
rfilter | Unmodulate temporal fluctuations by condition | ||
rmap | Map temporal fluctuations by condition | ||
roi | -b | print STDOUT ROI stats | |
run | Force execution of previous command options | ||
set | -Y | Set the value of internal variables | |
show | Show program status or values of data variables | ||
simulate | -y | ||
square | Clip to square images | ||
stability | -d | Generate plots of changes in image position and intensity | |
stabplots | Calculate displacements of center-of-mass | ||
stats | Calculate simple mean, stdev, and count statistics | ||
stdev | -V | Generate variance images | |
subset | -s | ||
surface | -S | Surface data | |
table | -t | Manipulate tables – lists of text and numbers | |
transform | -k | ||
ttest | -T | Generate activation maps based on t-test comparisons | |
variance | Generate variance images | ||
verbose | -v | Set program diagnostic and debugging flags | |
wait | -W | Wait for external events to synchronize data processing | |
warp | -X | ||
watch | -G | ||
writeover | -w | Write flag |
deleted
See Also:
fScan Home,
fScan Manual,
fScan Programming,
Manual Help