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jvs:fscan:manual:chapter2:roicorrel

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jvs:fscan:manual:chapter2:roicorrel [2016/07/26 20:17]
voyvodic 		jvs:fscan:manual:chapter2:roicorrel [2023/02/23 18:43] (current)
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 ===== ROI -- Define and manipulate Regions of Interest ===== ===== ROI -- Define and manipulate Regions of Interest =====
 ====usage:==== ====usage:====
- **-roi CORRELATE flag ref_roi binsize corr_roi  name thresh**\\+ ** -roi CORRELATE flag ref_roi binsize corr_roi  name thresh**\\
  ** -roi CORRELATE   2  dataset2 binsize corr_roi name thresh**\\  ** -roi CORRELATE   2  dataset2 binsize corr_roi name thresh**\\
- ** -roi CORRELATE   4  repeatleng refdelay corr_roi name thresh**+ ** -roi CORRELATE   4  repeatleng refdelay corr_roi name thresh skip**
   
 Generate new data set (named NAME) containing multiple Generate new data set (named NAME) containing multiple
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 BINSIZE is how many voxels in each dimension to bin together for reference (default=1). BINSIZE is how many voxels in each dimension to bin together for reference (default=1).
  
-REPEATLENG (if FLAG & 4) is the duration (secs) of the reference function -- assumes ref is repeated after this much time. Will calculate total number of REPEATLENG's in time series: +REPEATLENG, REFDELAY, SKIP are time values (secs) used for "half correlation" analysis (FLAG & 4).\\ 
-             NREPEATS = TotTime/REPEATLENG + * REPEATLENG - is the duration (secs) of the reference function -- assumes ref is repeated after this much time.  
-Length of half time series to be correlated will be:+ * REFDELAY - is the duration (secs) to ignore at beginning of data set (default = ~10s) 
 + * SKIP - is the amount of time (secs) to be ignored at the beginning of the data set (prior to first cycle) 
 + 
 +For half correlation analysis the number of full repeat cycles is first calcilated as: 
 +             NREPEATS = (TotTime-SKIP)/REPEATLENG 
 +The length of half time series to be correlated will be:
              HALFLENG = integer(NREPEATS/2) * REPEATLENG              HALFLENG = integer(NREPEATS/2) * REPEATLENG
-Will correlate first half: (REFDELAY:HALFLENG-1) to second half: (HALFLENG+REFDELAY:2*HALFLENG-1)+Will correlate first half: (SKIP+REFDELAY:SKIP+HALFLENG-1) to second half: (SKIP+HALFLENG+REFDELAY:SKIP+2*HALFLENG-1)
  
 CORR_ROI is the ROI to use as a mask for which voxels to test. By default,CORR_ROI is the entire data set.  Like REFROI, CORR_ROI can be the name of an ROI, or it can be: CORR_ROI is the ROI to use as a mask for which voxels to test. By default,CORR_ROI is the entire data set.  Like REFROI, CORR_ROI can be the name of an ROI, or it can be:
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  * 5 - correlate with every voxel in the data set volume (default)  * 5 - correlate with every voxel in the data set volume (default)
  * Neg value - specify any active ROI by the negative of its ROINUM  * Neg value - specify any active ROI by the negative of its ROINUM
- 
-REFDELAY (if FLAG & 4) is the duration (secs) to ignore at beginning of data set (default = ~10s) 
  
 NAME is the name of the output data set; default adds suffix roicorrel to current data set name. NAME is the name of the output data set; default adds suffix roicorrel to current data set name.
jvs/fscan/manual/chapter2/roicorrel.1469564230.txt.gz · Last modified: 2016/07/26 20:17 by voyvodic

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