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| jvs:fscan:manual:chapter2 [2011/08/02 19:39] – voyvodic | jvs:fscan:manual:chapter2 [2014/08/04 16:03] – external edit 127.0.0.1 |
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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]]| | | |
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| 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]]. |
| |[[jvs:fscan:manual:chapter2:create|create]]| |Create surface reconstructions or paint surfaces from images| | |[[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:delete|delete]]| |Delete a data set| |
| |[[jvs:fscan:manual:chapter2:designmatrix|designmatrix]]| |Create and manipulate task design matrix| | |[[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: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:display|display]]|-D|Specify display options| |
| |[[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| |
| |[[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| |
| |[[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]]| | | |
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| **See Also:**\\ | **See Also:**\\ |
