• -roi MEAN flag
• -roi CORREL flag refROI binsize corrROI name thresh
• -roi STATS refimage flag showflag [mode] name maskvalue [prefix prfxhdr] thresh nlevels level0 dlevel
• -roi STATS refimage flag showflag [mode] name maskvalue [prefix prfxhdr] thresh offroi ignoreroi onroi nlvls lvl0 dlvl
• -roi STATS refimage flag showflag [mode] name maskvalue [prefix prfxhdr] cycleleng cycle0 thresh

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)
• 0400 - weight average by overlay map values
• 01000 - ignore thresholds (default: use threshold if active)
• 02000 - calculate cycle-to-cycle variations (not with 010000 option)
• 04000 - binary mask; values above threshold are ON (default if no REFIMAGE)
• 010000 - threshhold curves; calculate stats for 10 different threshold values (see THRESHOLD note)
• 020000 - include negative values
• 040000 - show only non-zero values, not total voxel counts
• 1000000 - use threshold, even if THRESH is 0 (this is default if THRESH is non-zero)

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

• 1 - tab-separated columns in text output (default is space-separated)
• 2 - comma-separated columns in text output
• 3 - use space as separator
• 4 - do not write out stats (no stats file)
• 020 - include ROIs with 0 values in report
• 0100 - save as XML text file
• 0200 - save as non-XML text file
• 0300 - print in table format; lines identified by prefix
• 0400 - plot ref time series
• 01000 - save as ref time series
• 02000 - generate AMPLE statistics
• 04000 - print stats to 4 decimal points (defaul is 1 decimal)
• 010000 - show XYZ locs in ROOM coordinates)
• 020000 - show XYZ locs in Talairach coords (if available), or in Workspace 2 coords (if available)
• 040000 - put format ID on each line
• 0100000 - no output

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
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

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,

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