**fScan Reference Manual, Chapter 3 (KeyCmds:WinKeys): overlay ** ===== Overlay -- Manipulate overlay of images or surfaces onto each other ===== **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 [[jvs:fscan:manual:chapter2:surface|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:**\\ [[jvs:fscan|fScan Home]], [[jvs:fscan:manual|fScan Manual]], [[jvs:fscan:manual:chapter3|KeyCmds]], [[jvs:fscan:manual:chapter3:winkeys|WinKeys]], [[jvs:fscan:manual:help|Manual Help]]