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--- jvs:fscan:manual:chapter2:reference [2012/05/09 13:05]
voyvodic
+++ jvs:fscan:manual:chapter2:reference [2023/02/23 18:43]
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-**fScan Reference Manual, Chapter 2 (CmdLineOptions): reference**
-===== 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 "usage" line above shows only a few common modifiers. The complete list is:
--reference labels  LABEL1 LABEL2 ...\\
--reference codes  CODE1 CODE2 ...\\
--reference length  LENG1 LENG2 ...\\
--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   [ref0] MskRef\\
--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.)
-SCHEDULE is used to create a reference time course based on linked "schedule" files (see [[jvs:fscan:manual:chapter2:setschedule|-set schedule]]). Schedule files are typically in a 3-column text format indicating the onset and duration of different events; each file corresponds to a different type of event. Schedule files can be organized in groups to allow the events for a task to be separated in different ways.  Within a group, events should not overlap in time.  Schedule groups can be specified by either a number or a single letter. Three naming conventions are recognized for grouping schedules:\\
-     schXG_NAME          where G is a single letter and X is a number
-     sch_G_NAME          where G is a number or a single letter
-     sch_TG_NAME         where G is a number and T is any text not including '_'
-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 'a'. In general, if schedule files are organized in analysis groups the group should be specified explicitly when using the '-ref schedule' command.\\
-Examples of schedule file groupings would be:
-   sch6a_conda1.txt           sch_s1_firstgrp_cond1.txt
-   sch6a_conda2.txt           sch_s1_firstgrp_cond2.txt
-   sch6b_condb1.txt           sch_s2_scndgrp_cond3.txt
-   sch6b_condb2.txt           sch_s2_scndgrp_cond4.txt
-     -ref schedule b name schedb     (events labeled 'condb1' and 'condb2')
-     -ref schedule 1 name sched1     (events labeled 'firstgrp_cond1' & 'firstgrp_cond2'
-  The default group depends on what filenames have been linked.
-  If only the first column (sch6...) files were linked:
-     -ref schedule                   (only events labeled 'conda1' and 'conda2')
-  If only the second column (sch_s...) files were linked:
-     -ref schedule                   (all events)
-  If both columns above were linked, the default would include groups 'a', 1, and 2
-  (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', in which case the named REFNAME will be used automatically when appropriate.  A convolution can also be specified explicitly using '-reference convolve' as part of the reference definition.
-<code>
-    E.g.:  -ref hrffunc.txt name MyHRFunc
-           -ref 10 10s convolve MyHRFunc name MyTask
-</code>
-T-test convolutions are only fixed delays
-Note: Times for SKIP, DELAY, TOTAL, BIN, & LENGTH can be followed by 's' or 'i' (or 'S'/'I') to specify seconds or images (seconds is default).
-**See Also:**\\
-[[jvs:fscan:manual:chapter1:ilists|ILists]],
-[[jvs:fscan:manual:chapter1:eventlists|EventLists]],
-[[jvs:fscan:manual:chapter1:ilists|ILists]],
-[[jvs:fscan:manual:chapter1:queries|Queries]]
-[[jvs:fscan|fScan Home]],
-[[jvs:fscan:manual|fScan Manual]],
-[[jvs:fscan:manual:chapter2|CmdLineOptions]],
-[[jvs:fscan:manual:help|Manual Help]]

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