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jvs:fscan:manual:chapter2:reference [2012/06/12 21:12]
voyvodic 		jvs:fscan:manual:chapter2:reference [2023/02/23 18:43] (current)
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 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.\\ 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:\\+**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 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 sine CYCLESECS TOTSECS PHASESECS [SECSPERPOINT]\\
 -reference convolve [REF0] CONVREF\\ -reference convolve [REF0] CONVREF\\
 -reference mask   [REF0] MASKREF\\ -reference mask   [REF0] MASKREF\\
 +-reference correlate REF2\\
 +-reference response [FLAG]\\
 -reference schedule [GROUP]\\ -reference schedule [GROUP]\\
 -reference new\\ -reference new\\
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 ====Reading Schedule-format timing files==== ====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 '_'
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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==== ====Writing Schedule files====
 To write out a reference time course as a set of 3-column "schedule" files, use the following command: To write out a reference time course as a set of 3-column "schedule" files, use the following command:
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      Time    Value Duratn Label      Time    Value Duratn Label
-    0.000     1.0   30.0 rest +    0.000     1.0   10.0 rest 
-   30.000     2.0   10.0 taskon +   10.000     2.0   30.0 taskon 
-   40.000     3.0   30.0 rest +   40.000     3.0   10.0 rest 
-   70.000     2.0   10.0 taskon +   50.000     2.0   30.0 taskon 
-   80.000     1.0   30.0 rest +   80.000     1.0   10.0 rest 
-  110.000     2.0   10.0 taskon +   90.000     2.0   30.0 taskon 
-  120.000     3.0   30.0 rest+  120.000     3.0   10.0 rest
      
   To write MYREF out as schedule files you could use:   To write MYREF out as schedule files you could use:
     -ref myref write schedule sch3a     -ref myref write schedule sch3a
-  which would generate files: +  which would 2 generate files, sch3a_rest.txt and sch3a_taskon.txt: 
-    sch3a_rest.txt +     sch3a_rest.txt            sch3a_taskon.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> </code>
  
jvs/fscan/manual/chapter2/reference.1339535576.txt.gz · Last modified: 2014/08/04 16:03 (external edit)

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