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--- jvs:fscan:manual:chapter2 [2011/08/02 19:40]
voyvodic
+++ jvs:fscan:manual:chapter2 [2021/02/23 19:39]
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 **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]].
@@ Line 27: / Line 30: @@
 |[[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|
@@ Line 34: / Line 38: @@
 |[[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|
@@ Line 69: / Line 74: @@
 |[[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|
@@ Line 81: / Line 87: @@
 |[[jvs:fscan:manual:chapter2:query|query]]|-q| |
 |[[jvs:fscan:manual:chapter2:quit|quit]]| |  |
+|[[jvs:fscan:manual:chapter2:ramp|ramp]]| |Generate an intensity ramped image along a cardinal axis|
 |[[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|
@@ Line 88: / Line 95: @@
 |[[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|
@@ Line 96: / Line 104: @@
 |[[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:subset|subset]]|-s| |
 |[[jvs:fscan:manual:chapter2:surface|surface]]|-S|Surface data|
 |[[jvs:fscan:manual:chapter2:table|table]]|-t|Manipulate tables -- lists of text and numbers|
@@ Line 111: / Line 119: @@
 **deleted**
-|[[jvs:fscan:manual:chapter2:peek|peek]]| | |
+|[[jvs:fscan:manual:chapter2:peek|peek]]| |            |
 **See Also:**\\

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