Brain Imaging & Analysis Center

usage:

• “name”,Mo
• N,M,Fo
• Fo

The OVERLAY interactive command overlays one data set onto another. In general, any image data sets can be overlaid on each other. For example you can overlay images on images, surfaces on images, or images on surfaces. You cannot use OVERLAY, however, to combine surfaces together; to do that you use the SURFACE command. Overlaying only affects the displayed images, it does not modify either data set directly.

Overlay has many options for controlling how the overlay display should appear. By default, the display colors of each overlaid voxel are “or'd” with the colors of the underlying display. For example, when two gray-scaled images are overlayed it is often convenient to convert one image to red-scale and the other to green-scale, so that both images can be seen simultaneously without interfering with each other.

Usually, overlaying makes use of header information in each data set to figure out which location in the overlaid data set corresponds to each visible location in the underlying data set.

Usage options:
  o       Toggle overlay on/off
 Fo	    Set current active overlay flag to F
      F flag values
       1      overlay active
       2      hide underlay
       4      overlay is opaque (ignore translucence)
       8      turn on DIRECT flag
      16      show non-zero underlay opaque on top of overlays (for overlay on images),
              or show raw data values instead of display color (for overlay on surface)
      32      smooth overlay
      64      show overlay only where underlay is non-zero
     128      add underlay last, only show underlay where Olays==0
     256      hide overlay
     512      use fast version of overlay (for surface overlay on images)

    2048      CTRSMATCH - not used?
    4096      RESIZE - not used?
    8192      ZOOM - not used?toggle exceptions to default display
   16384      SLICESMATCH - not used?
 

“name”,M,Fo Set dataset NAME overlay mode M

  N,M,Fo      Set dataset num N overlay mode M
    Note:
      - overlay will be intialized if necessary
      - overlay becomes current active overlay
      - "name" can be used instead of all N's below
      - N=0, means previous window dataset (only for M=1)
 M:		MODE values
      0,Flg	attach overlay
          FLG:
            Octal values 4 - 04000 are used to toggle exceptions to default display
                   4 - make overlay opaque
                 010 - turn on DIRECT flag
                 020 - show non-zero underlay opaque on top of overlays (for overlay on images),
                          or show raw data values instead of display color (for overlay on surface)
                 040 - do not smooth overlay (default is to use smoothing filter)
                0100 - show overlay only where underlay is non-zero
                0200 - add underlay last, only show underlay where Olays==0
                0400 - hide overlay (create but do not display)
               01000 - use fast version of overlay (for surface overlay on images)
            Octal values > 010000 are used to explicitly specify transformation mode
               010000 - no transform -- simply match sizes
               020000 - one step transform matrix
               040000 - multi-step transform
      1       select overlay (0 is none)
      2       align overlay
      3       turn off align, keep align matrix
      3,0     turn off align, discard matrix
      3,Flg   (flg > 0) save align matrix in file
          FLG is format:
            1 - 4x4 matrix
            2 - register.dat (FreeSurfer)
            4 - FSL transform
          010 - stand-alone XML header w/ mtx
          020 - only write if non-identitty mtx
      4,flg,value 	set depth parameters for maximum intensity projection.
               The overlay value will be the maximum value in the
               overlay data set between Z0 and DEPTH mm of the 
               underlay surface.
               The displayed value will be the overlay value if that
               overlay voxel was on or above the underlay surface.
               For voxels below the surface, the displayed value will
                be a combination of surface and overlay value. The
                percentage of overlay displayed depends on the 
	  Translucence and Opacity parameters as:
		OPACITY > 0, TRANSLUCENCE > 0
		 PctSeen = 100 - OPACITY - voxDepth/TRANSLUCENCE
	 Note:
	   If the OPAQUE (4) overlay flag is set (see above),
	TRANSLUCENCE is ignored but surface OPACITY is not.
 
        FLG indicates which parameter to set to VALUE as:
           0 - Z0: mm above surface to include (default 0)
           1 - DEPTH: mm below surface to include (default 0)
          -1: all, above and below
          -2: ~1/2 the minimum (XYZ axis) thickness
               of the object (for olay on Surface)
           2 - TRANSLUCENCE: mm below surface that is visible.
              >0: overlay below surface fades to 0 at this depth
               0: special case, surface is transparent (equivalent
                  to infinite depth -- DEPTH is ignored)
              -1: special case, TRANSLUCENCE equals DEPTH (default)
           3 - OPACITY:% of overlay merged with surface image, prior
               to calculating effect of translucence (see above)
              100: overlay image at surface is opaque
               50: overlay at surface merged 50:50 with surface image
           4 - VSIZE: mm projected size of overlay voxel
               (default is to calculate vsize based on 
                voxel dimensions and projection angle)
           8 - add to Z0
           9 - add to DEPTH
          10 - add to TRANSLUCENCE
          11 - add to OPACITY
          16 - sub from Z0
          17 - sub from DEPTH
          18 - sub from TRANSLUCENCE
          19 - sub from OPACITY
 
          For Images, 'surface' is current slice
          For Surfaces: 'surface' is nearest surf
      5        copy alignment matrix from prev win to this
      5,1      copy alignmatrix from this win to all other open wins in WS
               with same XYZ dims as this win (except reference win)
      5,2      copy alignmatrix from this win to all other open wins in WS
               except reference win
      5,5      copy alignmatrix from this win to all other data sets in WS
               with same XYZ dims as this win (except reference win)
      5,6      copy alignmatrix from this win to all other data sets in WS
               except reference win
      6,rgb    use 24bit RGB value as color mask							
      6,r,g,b  use 8-bit R,G,B values as overlay color mask
      6,C,0    use code C (1=red,2=green,3=blue) as color mask
      7,rgb    same as F=6, but use color as underlay mask
      8,flg    reorder overlay
         FLG: 0 - move to bottom
              1 - move to top
              2 - move down 1
              3 - move up 1
  "name",9,flg,ptype	detach overlay
        NAME: name of new data set, if FLG > 0
        FLG: 0 - turn off overlay (default)
             1 - turn off all overlays
             2 - detach overlay as new dataset
             4 - detach underlay depth map as new dataset
             8 - detach overlay depth map as new dataset
            16 - detach underlay triangle map as new dataset
            (Note: flgs>1 only apply to olay on surface.
  10,f       toggle FLAG bit(s) F (see F values above)

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