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jvs:fscan:manual:chapter2:roicorrel

fScan Reference Manual, Chapter 2 (CmdLineOptions): roi

ROI -- Define and manipulate Regions of Interest

usage:

-roi CORRELATE flag ref_roi binsize corr_roi name thresh
-roi CORRELATE 2 dataset2 binsize corr_roi name thresh
-roi CORRELATE 4 repeatleng refdelay corr_roi name thresh skip

Generate new data set (named NAME) containing multiple
correlation maps based on correlating the time course for
each voxel within the REFROI in the current data set
with each voxel in the CORR_ROI. The 2 ROI's can be the same;
by default they are the entire data set volume.

FLAG can be used for specifying options (low 3 bits are MODE):
* 0 - Mode ALL: correlate every voxel in REF_ROI (seeds) with every voxel in CORR_ROI (targets)
* 1 - Mode LOCAL: generate neighbor correlation map. Correlates each voxel time course with its 26 neighbors and saves the mean correlation coefficient.
* 2 - Mode OTHER: generate inter-scan voxel correlation map. Correlates each voxel in this data set with same location in other data set. In this case REFROI is name of other data set.
* 4 - Mode HALF: correlate 1st half of each voxel time course w/ 2nd half
* 8 - include negative correlation values (usually set to 0)
* 16 - use REFROI as CORR_ROI as well (ignored if FLAG&3).
* 32 - do not mask out low intensity values (by default CORRELATE assumes the -m command)

REFROI specifieds the seed(s); can be the name of an ROI, or it can be:
* 0 - use the default: 5 if FLAG&
* 1 - use the time course at the current voxel as reference
* 2 - use the current point ROI time course as reference
* 3 - use every voxel within the current box roi as a separate reference (this generates 1 map per ref voxel; the ref voxel in each map will have correl value of 1.0)
* 4 - use every voxel in all active ROI's in this data set
* 5 - use every voxel in the volume
* neg value - specify any active ROI by the negative of its ROINUM

Default REFROI is 3 if there is a box ROI, otherwise it is 1

BINSIZE is how many voxels in each dimension to bin together for reference (default=1).

REPEATLENG, REFDELAY, SKIP are time values (secs) used for “half correlation” analysis (FLAG & 4).
* REPEATLENG - is the duration (secs) of the reference function – assumes ref is repeated after this much time.
* 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 

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:
* 0 - default. same as 5
* 1 - use REFROI as CORR_ROI
* 3 - use the current box roi as CORR_ROI
* 4 - correlate with voxels in all active ROI's in this data set
* 5 - correlate with every voxel in the data set volume (default)
* Neg value - specify any active ROI by the negative of its ROINUM

NAME is the name of the output data set; default adds suffix roicorrel to current data set name.

THRESH is the auto-correlation threshold for counting neighboring voxels as positively correlated (default=0.3)

See Also:
ROIs,
Create ROIs,
Edit ROIs,
Clusters,
ROI Stats

fScan Home,
fScan Manual,
CmdLineOptions,
Manual Help-roi CORRELATE flag ref_roi binsize corr_roi name thresh

jvs/fscan/manual/chapter2/roicorrel.txt · Last modified: 2016/07/26 21:05 by voyvodic