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jvs:fscan:manual:chapter2 [2011/08/02 19:40]
voyvodic
jvs:fscan:manual:chapter2 [2021/02/23 19:40] (current)
voyvodic
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 **Quick reference list** **Quick reference list**
-|[[jvs:​fscan:​manual:​chapter2:​accumulate|accumulate]]|[[jvs:​fscan:​manual:​chapter2:​adapt|adapt]]|[[jvs:​fscan:​manual:​chapter2:​ample|ample]]|[[jvs:​fscan:​manual:​chapter2:​average|average]]|[[jvs:​fscan:​manual:​chapter2:​convolve|convolve]]|[[jvs:​fscan:​manual:​chapter2:​correlate|correlate]]| +|[[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:​cpus|cpus]]|[[jvs:​fscan:​manual:​chapter2:​create|create]]|[[jvs:​fscan:​manual:​chapter2:​delete|delete]]|[[jvs:​fscan:​manual:​chapter2:​design|design]]|[[jvs:​fscan:​manual:​chapter2:​despike|despike]]|[[jvs:​fscan:​manual:​chapter2:​display|display]]+|[[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:​dmread|dmread]]|[[jvs:​fscan:​manual:​chapter2:​echo|echo]]|[[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:​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:​group|group]]|[[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:​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:​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:​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:​meanstdev|meanstdev]]|[[jvs:​fscan:​manual:​chapter2:​mean|mean]]|[[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:​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:​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:​phase|phase]]+|[[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:​physio|physio]]|[[jvs:​fscan:​manual:​chapter2:​plot|plot]]|[[jvs:​fscan:​manual:​chapter2:​query|query]]|[[jvs:​fscan:​manual:​chapter2:​reference|reference]]|[[jvs:​fscan:​manual:​chapter2:​regress|regress]]|[[jvs:​fscan:​manual:​chapter2:​reorder|reorder]]| +|[[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:​reslice|reslice]]|[[jvs:​fscan:​manual:​chapter2:​roi|roi]]|[[jvs:​fscan:​manual:​chapter2:​run|run]]|[[jvs:​fscan:​manual:​chapter2:​set|set]]|[[jvs:​fscan:​manual:​chapter2:​show|show]]|[[jvs:​fscan:​manual:​chapter2:​simulate|simulate]]+|[[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:​stability|stability]]|[[jvs:​fscan:​manual:​chapter2:​stats|stats]]|[[jvs:​fscan:​manual:​chapter2:​stdev|stdev]]|[[jvs:​fscan:​manual:​chapter2:​subset|subset]]|[[jvs:​fscan:​manual:​chapter2:​surface|surface]]|[[jvs:​fscan:​manual:​chapter2:​timebase|timebase]]| +|[[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:​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:​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:​writeover|writeover]]| | |+|[[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]]. 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]].
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 |[[jvs:​fscan:​manual:​chapter2:​accumulate|accumulate]]|-A|Accumulate values for calculating means, StDevs, and trial counts| |[[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:​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:​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:​ample|ample]]| |Generate AMPLE normalized activation maps and stability plots|
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 |[[jvs:​fscan:​manual:​chapter2:​browse|browse]]| |Select items from a list| |[[jvs:​fscan:​manual:​chapter2:​browse|browse]]| |Select items from a list|
 |[[jvs:​fscan:​manual:​chapter2:​chdir|chdir]]| |                            | |[[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:​connect|connect]]| |Open an external port connection|
 |[[jvs:​fscan:​manual:​chapter2:​convolve|convolve]]| |Convolve images using kernal matrix| |[[jvs:​fscan:​manual:​chapter2:​convolve|convolve]]| |Convolve images using kernal matrix|
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 |[[jvs:​fscan:​manual:​chapter2:​movie|movie]]| |Generate a time series data set from other data| |[[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:​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:​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:​output|output]]|-o|Write a data set to a disk file|
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 |[[jvs:​fscan:​manual:​chapter2:​resample|resample]]| | | |[[jvs:​fscan:​manual:​chapter2:​resample|resample]]| | |
 |[[jvs:​fscan:​manual:​chapter2:​reslice|reslice]]|-z|Resample a 3-D volume data set| |[[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:​rmap|rmap]]| |Map temporal fluctuations by condition|
 |[[jvs:​fscan:​manual:​chapter2:​roi|roi]]|-b|print STDOUT ROI stats| |[[jvs:​fscan:​manual:​chapter2:​roi|roi]]|-b|print STDOUT ROI stats|
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 |[[jvs:​fscan:​manual:​chapter2:​simulate|simulate]]|-y| | |[[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:​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:​stats|stats]]| |Calculate simple mean, stdev, and count statistics|
 |[[jvs:​fscan:​manual:​chapter2:​stdev|stdev]]|-V|Generate variance images| |[[jvs:​fscan:​manual:​chapter2:​stdev|stdev]]|-V|Generate variance images|
-|[[jvs:​fscan:​manual:​chapter2:​subset|subset]]|-s| | 
 |[[jvs:​fscan:​manual:​chapter2:​surface|surface]]|-S|Surface data| |[[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:​table|table]]|-t|Manipulate tables -- lists of text and numbers|
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 **deleted** **deleted**
-|[[jvs:​fscan:​manual:​chapter2:​peek|peek]]| | |+|[[jvs:​fscan:​manual:​chapter2:​peek|peek]]| |            |
  
 **See Also:**\\ **See Also:**\\
jvs/fscan/manual/chapter2.1312314015.txt.gz · Last modified: 2014/08/04 16:03 (external edit)