Brain Imaging & Analysis Center

Adding new ROIs

• -roi POINT [NAME] x y z
  
• -roi BLOCK [NAME] x0 y0 z0 nx ny nz
  
• -roi BLOCK [NAME] x0 y0 nx ny
  
• -roi BLOCK [NAME] x0 nx
  
• -roi CIRCLE [NAME] x0 y0 z0 rad
  
• -roi CIRCLE [NAME] x0 y0 rad
  
• -roi CIRCLE [NAME] x0 y0 z0 radx rady radz
  
• -roi ARROW [NAME] x0 y0 z0 x1 y1 z1
  
• -roi ARROW [NAME] x0 y0 x1 y1
  
• -roi ARROW [NAME] x0
  
• -roi TEXT [NAME] textstring x0 y0 z0 x1 y1 z1
  
• -roi TEXT [NAME] textstring x0 y0 x1 y1
• -roi MASK datasetname
• -roi FILE roifile
• -roi RX refimage (not yet implemented)
• -roi AVERAGE flag radiusMM thresh
• -roi HEAD [NAME] flag

   Create BLOCK roi by auto-detection of top, sides, & front/back of head.
   Arbitrarily set bottom by making I-S distance same as R-L.
    FLAG: 0 - default (bottom boundary set at top - (L/R distance)
          1 - 
        010 - set intensity threshold at 10% of maxval (default is 15%)
        020 - set     "         "     "  20%
           ...
        070 - set     "         "     "  70%

• -roi ALIGN [refimage flag refroi thisroi]

   Generate affine matrix (align or wsalaign) to align current images
   to REFIMAGE dataset by scaling and translating THISROI to match REFROI.
     REFIMAGE - data set to align to (prevwin by default)
     FLAG - option flag (default = 0)
     REFROI - name or ROINUM for REFIMAGE roi to use
              (default is active or first ROI)
     THISROI - name or ROINUM for current image roi
              (default is active or first).
   Example usage is to align head rois (see: -roi HEAD)

Generate ROI correlations

• -roi CORREL flag refROI binsize corrROI name thresh

Cluster ROIs

• -roi CLUSTER refimage flag name
• -roi MERGE refimage flag name minvalley minsize mindist

Generate ROI statistics

• -roi STATS refimage flag showflag mode name value nlevels level0 dlevel
• -roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh

Modifying ROIs

The RX type of ROI (when implemented) creates a slice prescription ROI on the current data set based on slice orientation in REFIMAGE.

The CLUSTER type ROI assumes that the current data set is an ROI mask image (in which regions are defined by voxels with the same intensity value). The CLUSTER command uses the input mask image to create an ROI list (name=NAME) of CLUSTER type ROIs where each cluster is defined by its mask value. For each CLUSTER, the center-of-mass location and the radius along the 3 principal axes are stored. By default, the new ROI list is attached to the input mask data set.

• REFIMAGE, find peak intensity value and voxel location.
• FLAG: (no values yet)
• NAME: name of ROI list. If omitted, the list is linked to input mask images.

The ROI command can also be used to manipulate existing ROI's.

-roi CLUSTER refimage flag name

	Assumes roi mask image as input.
Create an ROI list (name=NAME) of clusters where each
  cluster is defined by its mask value. For each cluster,
  store center-of-mass and radius along principal axes.
If REFIMAGE, find peak intensity value and voxel location.
By default, ROI list is attached to input mask images. 
FLAG: (no values yet)

NAME: name of ROI list. If omitted, list is linked to 
        input mask images.  

-roi MERGE refimage flag name minval minsize mindist

Assumes input data set is roi mask image with an ROI cluster list (usually made with ROI CLUSTER command). The ROI MERGE command allows you to modify the input data set and/or its Cluster list.

Merge can be used in different ways (controlled by FLAG):

FLAG 1 - Merge adjacent clusters if: 
  1) distance bet peaks < MINDIST
  2) stat value in valley between peaks is within MINVAL percent of lower peak
  3) smaller cluster contains fewer than MINSIZE voxels
FLAG 2 - Compare input cluster list to REFIMAGE cluster list.

FLAG 3 - Compare input cluster list to mask ROIs in REFIMAGE.

REFIMAGE is the reference data set; the type of data depends on FLAG:
  FLAG 1 - REFIMAGE is a voxel intensity map (e.g. tval map)
  FLAG 2 - REFIMAGE is another mask image with attached cluster list.
  FLAG 3 - REFIMAGE contains ROI images, typically an Atlas ROI map.
  FLAG 4 - Remove clusters containing less than MINVAL voxels
  FLAG 5 - Use REFIMAGE to adjust cluster index values. For each cluster, find
           REFIMAGE mask value (REFVALUE) at cluster center. New cluster index is:
                   REFVALUE * MINVAL + I
           where I starts at 1 and increments to ensure each cluster has unique index.

Other FLAG values:
  8 - do not modify input mask image values when editting ROI list; by default
      when ROI clusters are merged or cluster VALUEs are changed, the corresponding 
      image voxel values are also changed to match the new cluster VALUEs.
 16 - sort cluster list values by peak location (LPI -> RAS)
 32 - sort cluster list by cluster size (largest to smallest)

NAME: name of ROI list. If omitted, list is linked to input mask images.

-roi STATS refimage flag showflag mode name value nlevels level0 dlevel
-roi STATS refimage flag showflag mode name value cycleleng cycleoff thresh (if flag TIMESERIES)

Calculate 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 - TIMESERIES; calculate 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 - WEIGHTED; weight stats by mask value
 01000 - no threshold
 02000 - CYCLES; calculate time-series stats by task cycle
 04000 - BINARYMASK; consider all non-zero voxels in mask as single ROI 
 
SHOWFLAG - Report generation flags
     1 - tab-separated columns in text output
         (default is space-separated)
     2 - comma-separated columns in text output
  0100 - save as XML text file
  0200 - save as tab-delimited 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 > 0, only calculate for this mask value

If FLAG & 02010, time-series by CYCLE,  
  CYCLELENG: task cycle length in secs
  CYCLEOFF: first cycle offset in secs (ignore images before this)
  THRESH: mask threshold (assumes WEIGHTED and BINARYMASK)
otherwise,
  NLVLS: # threshold levels to calc separately (def=1)
  LEVEL0: first threshold level (def=0)
  DLEVEL: increment between levels (def=1)

If input is a Surface:
FLAG
  1 - surface area of AREA ROI or path length of contour ROI
  

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

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