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jvs:fscan:manual:chapter2:movie

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 delay binsize skip flag
  • -movie 'mean' duration ref name wsiz delay binsize skip flag
  • -movie 'stdev' duration ref name wsiz delay binsize skip flag
  • -movie 'meanstdev' duration ref name wsiz delay binsize skip flag
  • -movie 'accumulate' duration name wsiz delay binsize skip flag
  • -movie 'ttest' duration ref name wsiz delay binsize skip flag
  • -movie 'correl' duration ref name wsiz delay binsize skip flag
  • -movie 'fft' duration frequency [fftflg] name wsiz
  • -movie 'phase' duration name wsiz phaseoffset phasebin phasemax
  • -movie 'subset' duration ref name …
  • -movie 'images' imagelistfile [newbxhfile]

The MOVIE command creates a time series data set. Most usage options involve processing an existing image data set to create a new time series of a specified duration (in seconds). The FUNC argument specifies what type of image processing to do. If FUNC is 'images' the MOVIE command creates a new BXH style XML file (NEWBXHFILE) made of a time series of JPEG images as described in an existing text file list (see “Movie Images” below.)

Movies are generated by averaging images across multiple epochs within a time series, where each epoch is defined by a DURATION 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 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.

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 ($TRES) by default.
The number of frames generated in the output movie is DURATION/BINSIZE.

The SKIP argument allows you to skip some time at the beginning of the data set (in case there are start-up transient signals).

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 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.

Movie Images

The 'images' function is an unusual form of the MOVIE command. It creates an image data set out of a list of JPEG files. The command expects 2 filename arguments:

  • imagelistfile - the name of an existing text file containing a list of JPEG file names and presentation times (see ImageList Format below)
  • newbxhfile - the name of the new BXH style XML file to create describing the image time series data set (default: IMAGELISTFILE.bxh)

ImageList Format:
The ImageList is a plain text file with lines that contain a JPEG file name and its onset time. Any line that does not start with the name of a valid JPEG file will be ignored. Two different syntax forms are recognized:

  • 2 entries per line - the first is the JPEG file name, and the second is the image onset time in seconds.
  • 4 or more entries per line - the file is assumed to be in the form of a CIGAL paradigm input file (CIGAL PPF)
    • the first item is the JPEG file name
    • the 4th item is the image onset time in milliseconds
    • the 5th (optional) is the image duration in milliseconds
    • if the onset time is negative, then that image onset will be calculated as the end of the previous image (i.e. previous image onset plus previous duration).

The Movie Images command simply converts the ImageList file to a BXH file; it does not load the new data set.

See Also:
fScan Home,
fScan Manual,
CmdLineOptions,
Manual Help

jvs/fscan/manual/chapter2/movie.txt · Last modified: 2014/08/04 16:03 (external edit)