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jvs:fscan:manual:chapter2:reference [2012/05/09 13:14] voyvodic |
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- | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
- | ===== Reference -- Specify timing information===== | ||
- | == usage: -reference length LENG1 LENG2 ... labels LABEL1 LABEL2 ... delay DELAYTIME skip SKIPTIME (etc.) == | ||
- | ==== ==== | ||
- | *REFERENCE has many modifiers, which can be combined in a single -REF command or listed in separate -REF commands within a single command line. The " | ||
- | |||
- | -reference labels | ||
- | -reference codes CODE1 CODE2 ...\\ | ||
- | -reference length | ||
- | -reference skip SKIPTIME\\ | ||
- | -reference delay DELAYTIME\\ | ||
- | -reference total TOTALTIME\\ | ||
- | -reference bin BINSIZE\\ | ||
- | -reference cycles\\ | ||
- | -reference events\\ | ||
- | -reference starts\\ | ||
- | -reference hrf Latency\\ | ||
- | -reference hrf Latency Transition\\ | ||
- | -reference hrf Latency Rise Width Fall [Undershoot Recovery]\\ | ||
- | -reference hrf Latency Dip Depth Rise Width Fall Undershoot Recovery\\ | ||
- | -reference name REFNAME\\ | ||
- | -reference expand [ref0] [Npts]\\ | ||
- | -reference convolve [ref0] ConvRef\\ | ||
- | -reference mask | ||
- | -reference schedule [group]\\ | ||
- | -reference new\\ | ||
- | ==== ==== | ||
- | *SKIP -The amount of time to ignore at the beginning of the time series | ||
- | *DELAY -Indicates how much to shift each data point in time before applying the reference. | ||
- | |||
- | For blocks or cycles, only 1 full cycle needs to be specified; it will be expanded by repetition to fill the total time series being analyzed. (EXPAND can be specified to force expansion during creation.) | ||
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- | SCHEDULE is used to create a reference time course based on linked " | ||
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- | | ||
- | | ||
- | NAME above can be any condition label that makes sense to you. If the filename ends in " | ||
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- | The default schedule group includes any schedule files that do not match the above naming convention, or for which G is either a number or the letter ' | ||
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- | Examples of schedule file groupings would be: | ||
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- | | ||
- | | ||
- | | ||
- | | ||
- | -ref schedule b name schedb | ||
- | -ref schedule 1 name sched1 | ||
- | | ||
- | The default group depends on what filenames have been linked. | ||
- | If only the first column (sch6...) files were linked: | ||
- | -ref schedule | ||
- | If only the second column (sch_s...) files were linked: | ||
- | -ref schedule | ||
- | If both columns above were linked, the default would include groups ' | ||
- | (almost certainly not what you want). | ||
- | |||
- | For some statistics (t-test, correl), reference time course may be convolved with a canonical response function (e.g. hemodynamic response) before being used. The RF can be specified globally using '-set convolve REFNAME', | ||
- | < | ||
- | E.g.: -ref hrffunc.txt name MyHRFunc | ||
- | -ref 10 10s convolve MyHRFunc name MyTask | ||
- | </ | ||
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- | T-test convolutions are only fixed delays | ||
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- | Note: Times for SKIP, DELAY, TOTAL, BIN, & LENGTH can be followed by ' | ||
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- | **See Also:**\\ | ||
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