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 '_'

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     (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.

    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

fScan Home, fScan Manual, CmdLineOptions, Manual Help