Brain Imaging & Analysis Center

• 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 -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'  

If only the first column (sch6…) files were linked, the default would just include group 'a':

1. ref schedule (events labeled 'conda1' and 'conda2')

If only the second column (sch_s…) files were linked, the default would include all groups. 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.

    E.g.:  -ref hrffunc.txt name MyHRFunc
           -ref 10 10s convolve MyHRFunc name MyTask

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:
ILists, EventLists, ILists, Queries

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