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 name | Alias | Description |
---|---|---|
accumulate | -A | Accumulate values for calculating means, StDevs, and trial counts |
adapt | ||
addtime | Convert 3D images to 4D images | |
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 | |
chdir | ||
config | Set parameter values at startup | |
connect | Open an external port connection | |
convolve | Convolve images using kernal matrix | |
copy | ||
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 | |
designmatrix | Create and manipulate task design matrix | |
despike | Count and/or remove signal spikes from time course data | |
display | -D | Specify display options |
dmread | Read DM format files (pdigms etc) | |
echo | -E | Echo command arguments, substituting variable values |
events | ||
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 |
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 | |
ignore | ||
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 |
mean | -M | Generate mean images |
meanstdev | ||
menu | -K | |
mip | ||
movie | Generate a time series data set from other data | |
normalize | -N | Normalize intensities to a constant mean |
omit | Omit some task cycles when analyzing data | |
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 | ||
permute | ||
phase | -P | Create a phase map |
physio | Analyze physiological waveforms | |
plot | -p | Plot data in a graph |
query | -q | |
quit | ||
raw | Save a copy of the input raw data prior to any processing steps | |
reference | -r | Specify timing information |
regress | -R | Map temporal fluctuations by condition |
rename | ||
reorder | -J | Rearrange the order in which data appears in a data set |
resample | ||
reslice | -z | Resample a 3-D volume data set |
resize | -s | |
rmap | Map temporal fluctuations by condition | |
roi | -b | print STDOUT ROI stats |
run | Force execution of previous command options | |
series | ||
set | -Y | Set the value of internal variables |
show | Show program status or values of data variables | |
simulate | -y | |
stability | -d | Generate plots of changes in image position and intensity |
start | Specify fScan one-time start-up options | |
stats | Calculate simple mean, stdev, and count statistics | |
stdev | -V | Generate variance images |
surface | -S | Surface data |
table | -t | Manipulate tables – lists of text and numbers |
tpictsignal | ||
transform | -k | |
ttest | -T | Generate activation maps based on t-test comparisons |
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