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--- jvs:fscan:manual:chapter3:imagekeys:overlay [2011/11/09 16:18]
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+++ jvs:fscan:manual:chapter3:imagekeys:overlay [2023/02/23 18:43]
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-**fScan Reference Manual, Chapter 3 (KeyCmds:WinKeys): overlay **
-===== Overlay -- Manipulate overlay of images or surfaces onto each other =====
-**usage:**\\
-  * **"name",Mo**
-  * **N,Mo**
-  * **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:
-  "name",Mo	Set dataset NAME overlay mode M
-    N,Mo		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)
-   o        Toggle overlay on/off
-   Fo	    Set current active overlay flag to F
-        F flag values
-      overlay active
-      hide underlay
-      overlay is opaque (ignore translucence)
-      turn on DIRECT flag
-      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)
-      smooth overlay
-      show overlay only where underlay is non-zero
-      add underlay last, only show underlay where Olays==0
-      hide overlay
-      use fast version of overlay (for surface overlay on images)
-      CTRSMATCH - not used?
-      RESIZE - not used?
-      ZOOM - not used?
-      SLICESMATCH - not used?
-   M:		MODE values
-,flg	attach overlay
-            FLG: 0 - no transform -- simply match sizes
-- one step transform matrix
-- multi-step transform
-       select overlay (0 is none)
-       align overlay
-       turn off align, keep align matrix
-,0     turn off align, discard matrix
-,flg   (flg > 0) save align matrix in file
-            FLG is format:
-- 4x4 matrix
-- register.dat (FreeSurfer)
-- FSL transform
-- stand-alone XML header w/ mtx
-- only write if non-identitty mtx
-,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:
-- Z0: mm above surface to include (default 0)
-- 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)
-- TRANSLUCENCE: mm below surface that is visible.
-                >0: overlay below surface fades to 0 at this depth
-: special case, surface is transparent (equivalent
-                    to infinite depth -- DEPTH is ignored)
-                -1: special case, TRANSLUCENCE equals DEPTH (default)
-- OPACITY:% of overlay merged with surface image, prior
-                 to calculating effect of translucence (see above)
-: overlay image at surface is opaque
-: overlay at surface merged 50:50 with surface image
-- VSIZE: mm projected size of overlay voxel
-                 (default is to calculate vsize based on
-                  voxel dimensions and projection angle)
-- add to Z0
-- add to DEPTH
-- add to TRANSLUCENCE
-- add to OPACITY
-- sub from Z0
-- sub from DEPTH
-- sub from TRANSLUCENCE
-- sub from OPACITY
-            For Images, 'surface' is current slice
-            For Surfaces: 'surface' is nearest surf
-        copy alignment matrix from prev win to this
-,1      copy alignmatrix from this win to all other open wins in WS
-                 with same XYZ dims as this win (except reference win)
-,2      copy alignmatrix from this win to all other open wins in WS
-                 except reference win
-,5      copy alignmatrix from this win to all other data sets in WS
-                 with same XYZ dims as this win (except reference win)
-,6      copy alignmatrix from this win to all other data sets in WS
-                 except reference win
-,rgb    use 24bit RGB value as color mask
-,r,g,b  use 8-bit R,G,B values as overlay color mask
-,C,0    use code C (1=red,2=green,3=blue) as color mask
-,rgb    same as F=6, but use color as underlay mask
-,flg    reorder overlay
-           FLG: 0 - move to bottom
-- move to top
-- move down 1
-- move up 1
-    "name",9,flg,ptype	detach overlay
-          NAME: name of new data set, if FLG > 0
-          FLG: 0 - turn off overlay (default)
-- detach underlay as new dataset
-- detach overlay as new dataset
-- detach underlay depth map as new dataset
-- detach overlay depth map as new dataset
-- detach underlay triangle map as new dataset
-              (Note: flgs>1 only apply to olay on surface.
-,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]]

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