Brain Imaging & Analysis Center

usage: mode,flags h (see below for variations)

ROIMENU -- manipulate ROI interactively ('h')

  h                   toggle ROI flag
  0h                  turn off roi
  0,1h                list active ROIs for this window
  0,2h                list all active ROIs
  1h                  turn on roi
  'text',1 h          add text to current ROI
  1,type h            set default roi type (for subsequent ROIs)
  2h                  select ROI (nearest cursor)
  2,flag h            select ROI with options
  2,flag,num h        select ROI by number
  'name',2,flag h	select ROI by NAME
  'name',2,flag,locnum h  select and save ROI location
  2,flag,num,locnum h select ROI by NAME
    FLAG: 0  deselect -- make no ROI active
      1  select ROI as active
      2  select and open ROI for editting
      4  save ROI 1st point in savedLoc Locnum
      5  save ROI 2nd point in savedLoc Locnum
      6  save ROI active point in savedLoc Locnum
      7  save ROI stats Peak point in savedLoc Locnum
    NUM:	select ROI by number explictly.
      Numbering is order for this window (see 0,1h).
      If NUM is 0 or omitted:
        For flag < 4, find ROI at cursor (edge or center)
        For flag 4-6, use current selected ROI
    LOCNUM:  Saved Location number (1-NSAVEDLOCS) 					

  'name'3,type h      start new roi (and give it a name)
  3 h                 start new roi of default type
  3,type h            create roi interactively
  3,type,x1,y1,z1 h   create pt roi explicitly
  3,type,x1,y1,z1,x2,y2,z2 h  create block roi explicitly
  3,type,x1,y1,z1,xs,ys,zs h  create circle roi explicitly
  3,type,loc1 h       create pt roi using saved loc
  3,type,loc1,loc2 h  create roi using saved locs
  3,type,loc1,xs,ys,zs h   create roi using saved loc
   TYPE:
     0    duplicate most recent ROI to current cursor (& edit)
     1    single point in 3-D space
     2    start and end points of arrow 
     3    block -- rectangular volume in 3D or 4D
          corner and 3 lengths, t0 and nt (3D if nt==0)
     5    3d cross: ctr pt and 3 lengths
     6    3-D elliptical volume: ctr pt and 3 radii
     7    path -- linked points in space
     8    polygon -- closed path (perimeter on surface)
     9    slice polygons -- separate path drawn in each slice
    10    shell -- pts on perimeter of 3-D region
    11    area -- perimeter and all internal points
    12    shell -- perimeter and all internal points
    13    mask -- 2-D areas in image slices
   LOCn
      0    - current cursor location	
     1-10  - stored location N (1-NSAVEDLOCS [1-10])

  4 h                 stop editting and save current roi
  'name',4h           save current marked roi as 'name'
  5h                  set roi parameters
  5,r,g,b h           set color to R,G,B
  'color',5h          set color to "color"
  5,rgb h             set color to RGB (0xRRGGBB)
  5,0,flag h          set current roi flag to FLG
  5,1,flag h          turn on FLG bits in current roi flag
  5,2,flag h          toggle FLG bits in current roi flag
    FLAG values:
      1 - Hide this ROI (don't draw, don't use)
      4 - Fill interior of ROI when drawing
      8 - Treat circular ROI as cylinder in 3D (default is sphere)
  5,3,val h	        set ROI 'value' to val (default is roi num for data set)
  5,4,0 h  	        set polygon seed pt to current cursor location
  5,4,x,y,z h         set polygon seed pt to specified dataset xyz location
  5,5,0 h             set contour slice seed pt to current cursor location
  5,5,x,y,z h         set contour slice seed pt to specified dataset xyz location
  5,6,a h             set current roi adjuster param to A
  5,7,n h             set 4th dim low to N (t0 for Block, nsteps for Circle)
  5,8,n h             set 4th dim high to N (t1 for Block)
  5,9 h               move vtx to nearest previous (not immediate neighbor)
  6h                  copy ROIs from previous window
  'name',6            copy ROIs from named dataset/window
  7h                  edit roi
  7,0,n h             erase last N points in path (N=0 for all)
  7,2,wid,flag h      convert arrow roi to rectangular polygon
     FLAG: 1 - center polygon at arrow tip
           4 - fill polygon
  7,6,n,flag h        convert elliptical roi to N concentric steps 
     FLAG: 1 - inner rois increment r->value
           2 - decrement color from max in ctr to 1/2 of original in outermost ring
           4 - fill each ring
           8 - don't link inner rois to original
          16 - reverse increment/decrement sense (with flag 1 or 2)
  7,90 h              delete current roi for this window
  'name'7,90 h        delete named roi for this window
  7,99 h              delete all rois for this window

  8h                  calculate roi stats
  'name'8,flag,flag2,mod,val,nlvls,lvl0,dlvl h
      save stats in NAME, if present
    FLAG - stat calculation options
      1 - mean of voxels
      2 - stdev of voxels 
      4 - include N voxels for each time point
    010 - mean time course
    020 - calculate laterality index if available
    040 - only use non-zero voxels for stats
    FLAG2 - report generation options
    020 - include zero voxel ROI's in report
   0100 - save as XML text file
   0200 - save as tab-delimited text file

    MOD
      0 - default: 1 if active ROI, 2 if this has glossary, 4 if prev is atlas, 3 if prev has glossary
      1 - block ROI's (active or all)
      2 - mask values in current data
      3 - mask values in prev data set
      4 - atlas areas
    VAL: if > 0, only calculate for this mask value
    NLVLS: # threshold levels to calc separately (def=1)

  'name',9 h          write ROIs to file NAME
   9,0 h              write saved ROIs to file ("rois.txt" by default)
   9,nbits,flg,val h  write filled ROIs' values to data set
      NBITS: < 8 -> values are written as low (mask) bits in current data set
            8,16,24,32 -> values are written to new data set
      FLG:	1	write roi values (default, write roi color if
		 NBITS >= 8; otherwise roi->value)
        2   write roi color
	4	write VAL
	8	OR values from different ROIs
      VAL:  Value to write if (FLG & 4)
   10h                auto roi for surfs
   10,1h              surf: expand path to geodesic list
   10,2h              surf: mark all vertices inside path with parm and color
   10,3h              surf: expand path to include all inside vertices	   
   10,4h              surf: paint roi color onto vertices

   11h                Sample values in a region (ROI or near cursor)
   'name',11,flg,roinum,dist,thresh h 
      FLG: 1 - sample around (most recent) cursor loc
               otherwise sample activeroi (if active)
           2 - sample only thresholded voxels, if threshold active
           4 - sample only non-zero voxels
           8 - sample all contiguous (thresholded/non-zero) voxels
      DIST: Distance (in mm) to sample around cursor loc (0=no limit).
            If DIST > 0, FLG bit 1 is ignored.
      THRESH: Only sample voxels at or above THRESH (implies FLG 2).
      NAME: If input is time series, result is reference array, NAME.
            Single value result (or 1st val of time series) is stored
            in number variable $SAMPLE, regardless of NAME.	

  12h	                generate sliceRx ROI from slice Rx of prev window

See Also:
fScan Home, fScan Manual, KeyCmds, WinKeys, Manual Help