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**fScan Reference Manual, Chapter 2 (CmdLineOptions): Contents **

===== Command Line Options -- Summary List =====

**Quick reference list**
|[[jvs:fscan:manual:chapter2:accumulate|accumulate]]|[[jvs:fscan:manual:chapter2:adapt|adapt]]|[[jvs:fscan:manual:chapter2:align|align]]|[[jvs:fscan:manual:chapter2:ample|ample]]|[[jvs:fscan:manual:chapter2:average|average]]|[[jvs:fscan:manual:chapter2:bandpass|bandpass]]|
|[[jvs:fscan:manual:chapter2:blocks|blocks]]|[[jvs:fscan:manual:chapter2:browse|browse]]|[[jvs:fscan:manual:chapter2:chdir|chdir]]|[[jvs:fscan:manual:chapter2:connect|connect]]|[[jvs:fscan:manual:chapter2:convolve|convolve]]|[[jvs:fscan:manual:chapter2:copy|copy]]|
|[[jvs:fscan:manual:chapter2:correlate|correlate]]|[[jvs:fscan:manual:chapter2:cpus|cpus]]|[[jvs:fscan:manual:chapter2:create|create]]|[[jvs:fscan:manual:chapter2:delete|delete]]|[[jvs:fscan:manual:chapter2:design|designmatrix]]|[[jvs:fscan:manual:chapter2:despike|despike]]|
|[[jvs:fscan:manual:chapter2:display|display]]|[[jvs:fscan:manual:chapter2:dmread|dmread]]|[[jvs:fscan:manual:chapter2:echo|echo]]|[[jvs:fscan:manual:chapter2:events|events]]|[[jvs:fscan:manual:chapter2:execute|execute]]|[[jvs:fscan:manual:chapter2:expression|expression]]|
|[[jvs:fscan:manual:chapter2:fft|fft]]|[[jvs:fscan:manual:chapter2:fithrf|fithrf]]|[[jvs:fscan:manual:chapter2:glm|glm]]|[[jvs:fscan:manual:chapter2:header|header]]|[[jvs:fscan:manual:chapter2:help|help]]|[[jvs:fscan:manual:chapter2:history|history]]|
|[[jvs:fscan:manual:chapter2:if|if]]|[[jvs:fscan:manual:chapter2:ignore|ignore]]|[[jvs:fscan:manual:chapter2:images|images]]|[[jvs:fscan:manual:chapter2:input|input]]|[[jvs:fscan:manual:chapter2:join|join]]|[[jvs:fscan:manual:chapter2:list|list]]|
|[[jvs:fscan:manual:chapter2:lowfreq|lowfreq]]|[[jvs:fscan:manual:chapter2:mask|mask]]|[[jvs:fscan:manual:chapter2:mean|mean]]|[[jvs:fscan:manual:chapter2:meanstdev|meanstdev]]|[[jvs:fscan:manual:chapter2:menu|menu]]|[[jvs:fscan:manual:chapter2:movie|movie]]|
|[[jvs:fscan:manual:chapter2:normalize|normalize]]|[[jvs:fscan:manual:chapter2:options|options]]|[[jvs:fscan:manual:chapter2:output|output]]|[[jvs:fscan:manual:chapter2:overlay|overlay]]|[[jvs:fscan:manual:chapter2:paint|paint]]|[[jvs:fscan:manual:chapter2:pctsignal|pctsignal]]|
|[[jvs:fscan:manual:chapter2:peaks|peaks]]|[[jvs:fscan:manual:chapter2:permute|permute]]|[[jvs:fscan:manual:chapter2:phase|phase]]|[[jvs:fscan:manual:chapter2:physio|physio]]|[[jvs:fscan:manual:chapter2:plot|plot]]|[[jvs:fscan:manual:chapter2:query|query]]|
|[[jvs:fscan:manual:chapter2:quit|quit]]|[[jvs:fscan:manual:chapter2:raw|raw]]|[[jvs:fscan:manual:chapter2:reference|reference]]|[[jvs:fscan:manual:chapter2:regress|regress]]|[[jvs:fscan:manual:chapter2:rename|rename]]|[[jvs:fscan:manual:chapter2:reorder|reorder]]|
|[[jvs:fscan:manual:chapter2:resample|resample]]|[[jvs:fscan:manual:chapter2:reslice|reslice]]|[[jvs:fscan:manual:chapter2:roi|roi]]|[[jvs:fscan:manual:chapter2:run|run]]|[[jvs:fscan:manual:chapter2:series|series]]|[[jvs:fscan:manual:chapter2:set|set]]|
|[[jvs:fscan:manual:chapter2:show|show]]|[[jvs:fscan:manual:chapter2:simulate|simulate]]|[[jvs:fscan:manual:chapter2:stability|stability]]|[[jvs:fscan:manual:chapter2:stats|stats]]|[[jvs:fscan:manual:chapter2:stdev|stdev]]|[[jvs:fscan:manual:chapter2:resize|resize]]|
|[[jvs:fscan:manual:chapter2:surface|surface]]|[[jvs:fscan:manual:chapter2:table|table]]|[[jvs:fscan:manual:chapter2:tpictsignal|tpictsignal]]|[[jvs:fscan:manual:chapter2:transform|transform]]|[[jvs:fscan:manual:chapter2:ttest|ttest]]|[[jvs:fscan:manual:chapter2:verbose|verbose]]|
|[[jvs:fscan:manual:chapter2:wait|wait]]|[[jvs:fscan:manual:chapter2:warp|warp]]|[[jvs:fscan:manual:chapter2:watch|watch]]|[[jvs:fscan:manual:chapter2:writeover|writeover]]| | |


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 [[jvs:fscan:manual:chapter2:options|Options]] command files, or interactively via the [[jvs:fscan:manual:chapter3:winkeys:go|Go]] command, [[jvs:fscan:manual:chapter1:menus|Menus]], or [[jvs:fscan:manual:chapter1:taskbars|Taskbars]].

For a general description of fScan command-line options and how they compare to interactive [[jvs:fscan:manual:chapter3|key commands]] see [[jvs:fscan:manual:chapter1:commands|fScan Commands]].
See the [[jvs:fscan:manual:chapter1:programming|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**^
|[[jvs:fscan:manual:chapter2:accumulate|accumulate]]|-A|Accumulate values for calculating means, StDevs, and trial counts|
|[[jvs:fscan:manual:chapter2:adapt|adapt]]| | |
|[[jvs:fscan:manual:chapter2:addtime|addtime]]| |Convert 3D images to 4D images|
|[[jvs:fscan:manual:chapter2:align|align]]| |Auto-align images by optimizing mutual information |
|[[jvs:fscan:manual:chapter2:ample|ample]]| |Generate AMPLE normalized activation maps and stability plots|
|[[jvs:fscan:manual:chapter2:average|average]]|-a|Average input voxels in space or time|
|[[jvs:fscan:manual:chapter2:bandpass|bandpass]]|-B| |
|[[jvs:fscan:manual:chapter2:blocks|blocks]]| |Specify block condition in 1 cycle|
|[[jvs:fscan:manual:chapter2:browse|browse]]| |Select items from a list|
|[[jvs:fscan:manual:chapter2:chdir|chdir]]| |                            |
|[[jvs:fscan:manual:chapter2:config|config]]| |Set parameter values at startup|
|[[jvs:fscan:manual:chapter2:connect|connect]]| |Open an external port connection|
|[[jvs:fscan:manual:chapter2:convolve|convolve]]| |Convolve images using kernal matrix|
|[[jvs:fscan:manual:chapter2:copy|copy]]| |                    |
|[[jvs:fscan:manual:chapter2:correlate|correlate]]|-C|Calculate temporal correlation coefficient activation maps|
|[[jvs:fscan:manual:chapter2:cpus|cpus]]|-Q|Distribute processing of large runs across multiple parallel processors|
|[[jvs:fscan:manual:chapter2:create|create]]| |Create surface reconstructions or paint surfaces from images|
|[[jvs:fscan:manual:chapter2:delete|delete]]| |Delete a data set|
|[[jvs:fscan:manual:chapter2:design|designmatrix]]| |Create and manipulate task design matrix|
|[[jvs:fscan:manual:chapter2:despike|despike]]| |Count and/or remove signal spikes from time course data|
|[[jvs:fscan:manual:chapter2:display|display]]|-D|Specify display options|
|[[jvs:fscan:manual:chapter2:dmread|dmread]]| |Read DM format files (pdigms etc)|
|[[jvs:fscan:manual:chapter2:echo|echo]]|-E|Echo command arguments, substituting variable values|
|[[jvs:fscan:manual:chapter2:events|events]]| |                              |
|[[jvs:fscan:manual:chapter2:execute|execute]]|-X|Execute other programs by launching a shell script|
|[[jvs:fscan:manual:chapter2:expression|expression]]|-e|Perform arithmetic expressions on whole data sets|
|[[jvs:fscan:manual:chapter2:fft|fft]]|-F|Perform a fast Fourier transform (FFT)|
|[[jvs:fscan:manual:chapter2:fithrf|fithrf]]| |Fit a hemodynamic response function to time series data|
|[[jvs:fscan:manual:chapter2:glm|glm]]|-g|General linear model statistics|
|[[jvs:fscan:manual:chapter2:header|header]]|-h|Output file format specifications|
|[[jvs:fscan:manual:chapter2:help|help]]|-?| |
|[[jvs:fscan:manual:chapter2:history|history]]|-H|Add file HIST to history|
|[[jvs:fscan:manual:chapter2:images|images]]|-I|Reconstruct images from raw data|
|[[jvs:fscan:manual:chapter2:if|if]]| |Test some condition before executing commands|
|[[jvs:fscan:manual:chapter2:ignore|ignore]]| |             |
|[[jvs:fscan:manual:chapter2:input|input]]|-i|Specify input image codes|
|[[jvs:fscan:manual:chapter2:join|join]]|-j|Join conditions COND2 ... with COND1|
|[[jvs:fscan:manual:chapter2:list|list]]|-l| |
|[[jvs:fscan:manual:chapter2:lowfreq|lowfreq]]| |Remove slow temporal fluctuations (detrend)|
|[[jvs:fscan:manual:chapter2:mask|mask]]|-m|Specify binary (byte) mask image for input|
|[[jvs:fscan:manual:chapter2:mean|mean]]|-M|Generate mean images|
|[[jvs:fscan:manual:chapter2:meanstdev|meanstdev]]| | |
|[[jvs:fscan:manual:chapter2:menu|menu]]|-K| |
|[[jvs:fscan:manual:chapter2:mip|mip]]| |            |
|[[jvs:fscan:manual:chapter2:movie|movie]]| |Generate a time series data set from other data|
|[[jvs:fscan:manual:chapter2:normalize|normalize]]|-N|Normalize intensities to a constant mean|
|[[jvs:fscan:manual:chapter2:omit|omit]]| |Omit some task cycles when analyzing data|
|[[jvs:fscan:manual:chapter2:options|options]]|-O|Read and execute a file containing fScan commands|
|[[jvs:fscan:manual:chapter2:output|output]]|-o|Write a data set to a disk file|
|[[jvs:fscan:manual:chapter2:overlay|overlay]]|-U| |
|[[jvs:fscan:manual:chapter2:paint|paint]]|-u| |
|[[jvs:fscan:manual:chapter2:pctsignal|pctsignal]]| | |
|[[jvs:fscan:manual:chapter2:peaks|peaks]]| | |
|[[jvs:fscan:manual:chapter2:permute|permute]]| |      |
|[[jvs:fscan:manual:chapter2:phase|phase]]|-P|Create a phase map|
|[[jvs:fscan:manual:chapter2:physio|physio]]| |Analyze physiological waveforms|
|[[jvs:fscan:manual:chapter2:plot|plot]]|-p|Plot data in a graph|
|[[jvs:fscan:manual:chapter2:query|query]]|-q| |
|[[jvs:fscan:manual:chapter2:quit|quit]]| |  |
|[[jvs:fscan:manual:chapter2:raw|raw]]| |Save a copy of the input raw data prior to any processing steps|
|[[jvs:fscan:manual:chapter2:reference|reference]]|-r|Specify timing information|
|[[jvs:fscan:manual:chapter2:regress|regress]]|-R|Map temporal fluctuations by condition|
|[[jvs:fscan:manual:chapter2:rename|rename]]| | |
|[[jvs:fscan:manual:chapter2:reorder|reorder]]|-J|Rearrange the order in which data appears in a data set|
|[[jvs:fscan:manual:chapter2:resample|resample]]| | |
|[[jvs:fscan:manual:chapter2:reslice|reslice]]|-z|Resample a 3-D volume data set|
|[[jvs:fscan:manual:chapter2:resize|resize]]|-s| |
|[[jvs:fscan:manual:chapter2:rmap|rmap]]| |Map temporal fluctuations by condition|
|[[jvs:fscan:manual:chapter2:roi|roi]]|-b|print STDOUT ROI stats|
|[[jvs:fscan:manual:chapter2:run|run]]| |Force execution of previous command options|
|[[jvs:fscan:manual:chapter2:series|series]]| | |
|[[jvs:fscan:manual:chapter2:set|set]]|-Y|Set the value of internal variables|
|[[jvs:fscan:manual:chapter2:show|show]]| |Show program status or values of data variables|
|[[jvs:fscan:manual:chapter2:simulate|simulate]]|-y| |
|[[jvs:fscan:manual:chapter2:stability|stability]]|-d|Generate plots of changes in image position and intensity|
|[[jvs:fscan:manual:chapter2:start|start]]| |Specify fScan one-time start-up options|
|[[jvs:fscan:manual:chapter2:stats|stats]]| |Calculate simple mean, stdev, and count statistics|
|[[jvs:fscan:manual:chapter2:stdev|stdev]]|-V|Generate variance images|
|[[jvs:fscan:manual:chapter2:surface|surface]]|-S|Surface data|
|[[jvs:fscan:manual:chapter2:table|table]]|-t|Manipulate tables -- lists of text and numbers|
|[[jvs:fscan:manual:chapter2:tpictsignal|tpictsignal]]| | |
|[[jvs:fscan:manual:chapter2:transform|transform]]|-k| |
|[[jvs:fscan:manual:chapter2:ttest|ttest]]|-T|Generate activation maps based on t-test comparisons|
|[[jvs:fscan:manual:chapter2:verbose|verbose]]|-v|Set program diagnostic and debugging flags|
|[[jvs:fscan:manual:chapter2:wait|wait]]|-W|Wait for external events to synchronize data processing|
|[[jvs:fscan:manual:chapter2:warp|warp]]|-X| |
|[[jvs:fscan:manual:chapter2:watch|watch]]|-G| |
|[[jvs:fscan:manual:chapter2:writeover|writeover]]|-w|Write flag|

**deleted**
|[[jvs:fscan:manual:chapter2:peek|peek]]| |            |

**See Also:**\\
[[jvs:fscan|fScan Home]],
[[jvs:fscan:manual|fScan Manual]],
[[jvs:fscan:manual:chapter1:programming|fScan Programming]],
[[jvs:fscan:manual:help|Manual Help]]
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