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--- jvs:fscan:manual:chapter2:movie [2011/03/31 14:49]
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+++ jvs:fscan:manual:chapter2:movie [2023/02/23 18:43]
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-**fScan Reference Manual, Chapter 2 (CmdLineOptions): movie**
-===== Movie -- Generate average timecourse movie=====
-**usage: -movie func duration name wsiz offset binsize flag**
-  * -movie            duration  ref name wsiz skip delay binsize flag\\
-  * -movie 'mean'       duration  ref name wsiz skip delay binsize flag\\
-  * -movie 'stdev'      duration  ref name wsiz skip delay binsize flag\\
-  * -movie 'meanstdev'  duration  ref name wsiz skip delay binsize flag\\
-  * -movie 'accumulate' duration  name wsiz skip delay binsize flag\\
-  * -movie 'ttest'      duration  ref name wsiz skip delay binsize flag\\
-  * -movie 'correl'     duration  ref name wsiz skip delay binsize flag\\
-  * -movie 'fft'        duration  frequency [fftflg] name wsiz\\
-  * -movie 'phase'      duration  name wsiz phaseoffset phasebin phasemax\\
-Movies can be generated by combining images across multiple time series, where each time series is defined relative to some starting event. If REF is specified it is the name of a reference time course and the movie starting events are event time points in REF. If no REF is specified, the starting event points are uniformly spaced every DURATION seconds.
-The SKIP argument allows you to skip some time at the beginning of the data set (in case there are start-up transient signals).\\
-The DELAY argument allows you to shift the starting events DELAY seconds before (negative DELAY values) or after (positive values) the REF (or every DURATION) time events.\\
-Note that SKIP and DELAY both affect which images are included at the beginning of the movie cycle, but in different ways. If you have a 24s cycle and you skip 6s, then your first cycle will start at time 0 but would ignore the first 6s so that cycle would only include 18s of data and your cycle start times would be at 0, 24s, 48s, etc. But if you have 24s cycle and you delay 6s, then your first cycle will start at time 6s, and all your cycles are shifted by 6s, with start times at 6s, 30s, 54s, etc.
-The BINSIZE argument lets you specify how many seconds of input image time points should be combined in each movie frame. By default, BINSIZE is 1 input image volume time point ([[jvs:fscan:manual:chapter4:tres|$TRES]]) by default.
-The number of frames generated in the output movie is DURATION/BINSIZE.
-The way a movie is generated is controlled by the FUNC name, which is a key word appearing as the first argument (not counting "verbose"). FUNC can be any of the following:
-  * mean - generate mean values across repeated duration cycles\\
-  * stdev - generate standard deviation values across repeated cycles\\
-  * meanstdev - generate mean and stedv values across repeated cycles as a 5-D data set\\
-  * accumulate - generate sum and sum of squares values across repeated  cycles as a 5-D data set\\
-  * ttest - \\
-  * correl -\\
-  * fft - Do 1D FFT
-    * extract power and phase at FREQUENCY, then for each voxel find movie group that is phase*DURATION/360 and put the power value in that group.\\
-  * phase - Convert a phase map to a movie\\
-    * DURATION bins of PHASEBIN degrees (out of PHASEMAX deg cycle)\\
-    * Movie frame 0 is at PHASEOFFSET
-Note: If "verbose" appears immediately after MOVIE (before the FUNC name), the command will display image sorting information before it executes.
-**See Also:**\\
-[[jvs:fscan|fScan Home]],
-[[jvs:fscan:manual|fScan Manual]],
-[[jvs:fscan:manual:chapter2|CmdLineOptions]],
-[[jvs:fscan:manual:help|Manual Help]]

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