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--- jvs:fscan:manual:chapter2:reference [2014/08/04 16:03]
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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. Arguments in lower case are reserved words entered as shown (or abbreviated); arguments in upper case are numbers or names that you supply.\\
-**The complete option 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 offset OFFSETTIME\\
--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] MASKREF\\
--reference schedule [GROUP]\\
--reference new\\
--reference REFNAME write schedule [PREFIX]
-==== ====
-  *SKIP -The amount of time to ignore at the beginning of the time series
-  *DELAY -Indicates the expected delay between the reference time and the signal response (e.g. hemodynamic delay)
-  *OFFSET -A fixed time offset to be added to every reference time point (e.g to correct global synchronization)
-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).
-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.)
-====Reading Schedule-format timing files====
-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 X is a number and G is a single letter
-     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 '_'
-NAME above can be any condition label that makes sense to you. If the filename ends in ".txt" that suffix will not be included in the label names.
-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_SECONDGRP_COND3.txt
-   sch6b_CONDB2.txt           sch_s2_SECONDGRP_COND4.txt
-     -ref schedule b name schedb     (loads events labeled 'CONDB1' and 'CONDB2')
-     -ref schedule 1 name sched1     (loads 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                   (loads only events labeled 'CONDA1' and 'CONDA2')
-  If the second column (sch_s...) files were linked the default would include multiple groups ('a', 1, and 2)
-  which is almost certainly not what you want.  If you link multiple schedule file groups to your data sets
-  you should probably explicitly specify which group you want when creating a new reference time course.
-====Writing Schedule files====
-To write out a reference time course as a set of 3-column "schedule" files, use the following command:
-<code>
-  -ref REFNAME write schedule [PREFIX]
-  Where REFNAME is the name of an existing reference time course (use $lastref to get the current active time course).
-  PREFIX is the filename prefix you want to use; the default PREFIX is "sch".
-</code>
-The REFNAME time course must have labels specified for the different conditions. For each condition label (CONDLABEL), a separate schedule file will be created, named: PREFIX_CONDLABEL.txt.
-<code>
-  For example, consider the sample reference time course named MYREF:
-  To view your reference time course use:
-    -show ref myref
-     Time    Value Duratn Label
-.000     1.0   10.0 rest
-.000     2.0   30.0 taskon
-.000     3.0   10.0 rest
-.000     2.0   30.0 taskon
-.000     1.0   10.0 rest
-.000     2.0   30.0 taskon
-.000     3.0   10.0 rest
-  To write MYREF out as schedule files you could use:
-    -ref myref write schedule sch3a
-  which would 2 generate files, sch3a_rest.txt and sch3a_taskon.txt:
-     sch3a_rest.txt            sch3a_taskon.txt
-.0    10.0   1            10.0   30.0   1
-.0    10.0   1            50.0   30.0   1
-.0    10.0   1            90.0   30.0   1
-.0    10.0   1
-</code>
-====Expanding or convolving a reference time course====
-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 use only fixed delays
-**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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