Brain Imaging & Analysis Center

• -roi MEAN flag
• -roi CORREL flag refROI binsize corrROI name thresh
• -roi STATS refimage flag showflag mode name value nlevels level0 dlevel

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)

• 0 - default stats (3 = Mean,Count,StDev)
• 1 - include mean
• 2 - include counts, and mean
• 3 - include stdev, and above
• 4 - include range, and above
• 5 - include ctr loc, and above
• 6 - include peak val&loc, and above
• 7 - include intensity weighted ctr loc, and above
• 010 - mean time course
• 020 - calculate laterality index if available
• 040 - calculate stats omitting zero values
• 0100 - report ROI volumes in mm3 (voxel count X voxel volume)
• 0200 - include ROI's with only zero values (usually ignored)

SHOWFLAG - Report generation flags

• 1 - tab-separated columns in text output (default is space-separated)
• 2 - comma-separated columns in text output
• 4 - do not write out stats (no stats file)
• 0100 - save as XML text file
• 0200 - save as non-XML text file
• 0400 - plot ref time series
• 01000 - save as ref time series
• 02000 - generate AMPLE statistics
• 04000 - ignore thresholds (default: use threshold if active)
• 010000 - Watch flag (?)

MODE

• 0 - default: 1 if active ROI, 2 if this has glossary, 3 if prev has glossary, 4 if prev is atlas
• 1 - block ROI's (active or all)
• 2 - mask values in current data
• 3 - mask values in prev data set
• 4 - atlas areas
• 8 - threshold (can combine with 1-4)

NAME - save stats in file NAME, if specified

VAL: If VAL > 0, only calculate for this mask value

NLVLS: Number threshold levels to calculate separately (default=1)

If input is a Surface:
FLAG

• 1 - surface area of AREA ROI or path length of contour ROI

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