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fScan Reference Manual, Chapter 2 (CmdLineOptions): roistats
Calulate stats in input data by ROI.
REFIMAGE - dataset to use as ROI mask(s)
FLAG - stats options (select one value 0-7; add other values)
THRESHOLD: THRESH arg is the lowest threshold and stepsize. If OFFROI is non-zero this will generate ROC curves. If IGNOREROI is non-zero, REFIMAGE voxels with that value are ignored. If ONROI is non-zero, only REFIMAGE voxels with that value are included.
SHOWFLAG - Report generation flags
MODE
NAME - save stats in file NAME, if specified
MASKVAL: If > 0, only calculate for this mask value
PREFIX: string prepended to each data line in report \
PRFXHDR: string prepended to column header lines in report
THRESH: explicit threshold level (default is current image threshold, or if FLAG&010000 default is 0.5)
OFFROI: if FLAG&010000, OFFROI is ROI value indicating true-negative voxels
IGNOREROI: if FLAG&010000, ROI value to ignore when making ROC curves
ONROI: if FLAG&010000, ROI value indicating true-positive voxels for ROC curves
NLVLS: Number threshold levels to calculate separately (default=1, or 10 if FLAG&010000)
Note: If you want a PREFIX without specifying output file NAME you must include a MASKVAL (0 for default) to avoid syntax confusion.
If input is a Surface:
FLAG
* 1 - surface area of AREA ROI or path length of contour ROI
====-roi CORRELATE flag ref_roi binsize corr_roi name thresh====
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:
* 1 - generate neighbor correlation map. Correlates each voxel time course with
its 26 neighbors and saves the mean correlation coefficient.
* 2 - do not mask out low intensity values (by default CORRELATE assumes the -m command)
* 4 - use REFROI as CORR_ROI as well
REFROI 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
one 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
* <0 - Negative ROINUM - specify any active ROI by the negative of its ROINUM
Default 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).
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)
* <0 - Negative ROINUM - 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,
fScan Home,
fScan Manual,
CmdLineOptions,
Manual Help