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jvs:fscan:manual:chapter2:reference [2012/05/09 13:13]
voyvodic 		jvs:fscan:manual:chapter2:reference [2023/02/23 18:43] (current)
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 == usage: -reference length LENG1 LENG2 ... labels LABEL1 LABEL2 ... delay DELAYTIME skip SKIPTIME (etc.) == == 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 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 labels  LABEL1 LABEL2 ...\\
 -reference codes  CODE1 CODE2 ...\\ -reference codes  CODE1 CODE2 ...\\
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 -reference total TOTALTIME\\ -reference total TOTALTIME\\
 -reference bin  BINSIZE\\ -reference bin  BINSIZE\\
 +-reference offset OFFSETTIME\\
 -reference cycles\\ -reference cycles\\
 -reference events\\ -reference events\\
 -reference starts\\ -reference starts\\
--reference hrf Latency\\ +-reference hrf LATENCY\\ 
--reference hrf Latency Transition\\ +-reference hrf LATENCY TRANSITION\\ 
--reference hrf Latency Rise Width Fall [Undershoot Recovery]\\ +-reference hrf LATENCY RISE WIDTH FALL [UNDERSHOOT RECOVERY]\\ 
--reference hrf Latency Dip Depth Rise Width Fall Undershoot Recovery\\+-reference hrf LATENCY DIP DEPTH RISE WIDTH FALL UNDERSHOOT RECOVERY\\
 -reference name REFNAME\\ -reference name REFNAME\\
--reference expand [ref0] [Npts]\\ +-reference expand [REF0] [TOTSECS SECSPERPOINT]\\ 
--reference convolve [ref0] ConvRef\\ +-reference sine CYCLESECS TOTSECS PHASESECS [SECSPERPOINT]\\ 
--reference mask   [ref0] MskRef\\ +-reference convolve [REF0] CONVREF\\ 
--reference schedule [group]\\+-reference mask   [REF0] MASKREF\\ 
 +-reference correlate REF2\\ 
 +-reference response [FLAG]\\ 
 +-reference schedule [GROUP]\\
 -reference new\\ -reference new\\
 +-reference REFNAME write schedule [PREFIX]
 ==== ==== ==== ====
   *SKIP -The amount of time to ignore at the beginning of the time series   *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.+  *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)
  
-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.)+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:\\ 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+     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_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 '_'      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. 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.\\+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: Examples of schedule file groupings would be:
    sch6a_CONDA1.txt           sch_s1_FIRSTGRP_COND1.txt    sch6a_CONDA1.txt           sch_s1_FIRSTGRP_COND1.txt
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    sch6b_CONDB2.txt           sch_s2_SECONDGRP_COND4.txt    sch6b_CONDB2.txt           sch_s2_SECONDGRP_COND4.txt
      
-     -ref schedule b name schedb     (events labeled 'CONDB1' and 'CONDB2') +     -ref schedule b name schedb     (loads events labeled 'CONDB1' and 'CONDB2') 
-     -ref schedule 1 name sched1     (events labeled 'FIRSTGRP_COND1' & 'FIRSTGRP_COND2'+     -ref schedule 1 name sched1     (loads events labeled 'FIRSTGRP_COND1' & 'FIRSTGRP_COND2'
      
   The default group depends on what filenames have been linked.   The default group depends on what filenames have been linked.
   If only the first column (sch6...) files were linked:   If only the first column (sch6...) files were linked:
-     -ref schedule                   (only events labeled 'CONDA1' and 'CONDA2') +     -ref schedule                   (loads only events labeled 'CONDA1' and 'CONDA2') 
-  If only the second column (sch_s...) files were linked: +  If the second column (sch_s...) files were linked the default would include multiple groups ('a', 1, and 2) 
-     -ref schedule                   (all events) +  which is almost certainly not what you want.  If you link multiple schedule file groups to your data sets 
-  If both columns above were linked, the default would include groups 'a', 1, and 2  +  you should probably explicitly specify which group you want when creating a new reference time course. 
-  (almost certainly not what you want).+  
 +====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 
 +    0.000     1.0   10.0 rest 
 +   10.000     2.0   30.0 taskon 
 +   40.000     3.0   10.0 rest 
 +   50.000     2.0   30.0 taskon 
 +   80.000     1.0   10.0 rest 
 +   90.000     2.0   30.0 taskon 
 +  120.000     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 
 +    0.0    10.0   1            10.0   30.0   1 
 +   40.0    10.0   1            50.0   30.0   1 
 +   80.0    10.0   1            90.0   30.0   1 
 +  120.0    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. 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> <code>
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 </code> </code>
  
-T-test convolutions are only fixed delays +T-test convolutions use 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:**\\ **See Also:**\\
jvs/fscan/manual/chapter2/reference.1336569216.txt.gz · Last modified: 2014/08/04 16:03 (external edit)

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