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jvs:fscan:manual:chapter2:reference [2012/05/09 13:05] 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 " | + | 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 " |
+ | **The complete option list is:**\\ | ||
-reference labels | -reference labels | ||
-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 | + | *DELAY -Indicates |
+ | *OFFSET -A fixed time offset to be added to every reference | ||
- | For blocks or cycles, only 1 full cycle needs to be specified; it will be expanded | + | Note: Times for SKIP, DELAY, TOTAL, BIN, & LENGTH can be followed |
+ | 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 is used to create a reference time course based on linked " | ||
- | | + | |
| | ||
| | ||
- | 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 ' | + | NAME above can be any condition label that makes sense to you. If the filename ends in " |
+ | |||
+ | 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 ' | ||
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 |
- | sch6a_conda2.txt sch_s1_firstgrp_cond2.txt | + | sch6a_CONDA2.txt sch_s1_FIRSTGRP_COND2.txt |
- | sch6b_condb1.txt sch_s2_scndgrp_cond3.txt | + | sch6b_CONDB1.txt sch_s2_SECONDGRP_COND3.txt |
- | sch6b_condb2.txt sch_s2_scndgrp_cond4.txt | + | sch6b_CONDB2.txt sch_s2_SECONDGRP_COND4.txt |
+ | |||
+ | -ref schedule b name schedb | ||
+ | -ref schedule 1 name sched1 | ||
| | ||
- | -ref schedule b name schedb | ||
- | -ref schedule 1 name sched1 | ||
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 | + | -ref schedule |
- | If only the second column (sch_s...) files were linked: | + | If the second column (sch_s...) files were linked the default would include |
- | -ref schedule | + | |
- | If both columns above were linked, | + | 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 " | ||
+ | < | ||
+ | -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 " | ||
+ | </ | ||
+ | The REFNAME time course must have labels specified for the different conditions. For each condition label (CONDLABEL), | ||
+ | |||
+ | < | ||
+ | For example, consider the sample reference time course named MYREF: | ||
+ | To view your reference time course use: | ||
+ | -show ref myref | ||
+ | |||
+ | | ||
+ | 0.000 | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | 120.000 | ||
+ | |||
+ | 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: | ||
+ | | ||
+ | 0.0 10.0 | ||
+ | | ||
+ | | ||
+ | 120.0 10.0 1 | ||
+ | </ | ||
+ | ====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', | 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', | ||
< | < | ||
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</ | </ | ||
- | T-test convolutions | + | T-test convolutions |
- | + | ||
- | Note: Times for SKIP, DELAY, TOTAL, BIN, & LENGTH can be followed by ' | + | |
**See Also:**\\ | **See Also:**\\ |