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--- jvs:fscan:manual:chapter3:winkeys:roi [2011/12/27 19:32] – voyvodic
+++ jvs:fscan:manual:chapter3:winkeys:roi [2012/02/22 17:54] – voyvodic
@@ Line 53: / Line 53: @@
     path -- linked points in space
     polygon -- closed path (perimeter on surface)
-    slice polygons -- separate path drawn in each slice
+    slice polygons -- separate polygon drawn in each slice
-    shell -- pts on perimeter of 3-D region
+    slice paths -- separate path drawn in each slice
     area -- perimeter and all internal points
     shell -- perimeter and all internal points
@@ Line 145: / Line 145: @@
 ,1,flg,dist h
                         expand path by interpolation
-          FLG  1 - add node for every voxel DIST step (default)
+          FLG  1 - reuse same ROI
 - interpolate contours for intervening slices
-          DIST   -- distance between node steps in mm (default: voxel width)
+               ? - add node for every voxel DIST step (default)
+          DIST   - distance between node steps in mm (default: voxel width)
+                 - Flg 2: distance between contours in mm (default: voxel depth)
 ,2,flg,dist,val h
                         sample image perpendicular to path at each node;
-                        find edge VAL, edge is values near OUTVAL;
+                        find edge where image intensity crosses VAL boundary,
                         move node to edge if found; flag nodes where no edge found
+          FLG  1 - reuse same ROI (default is create new ROI)
+- edge is intensity change >= VAL %
+- only look for edge on one side
+                   (default is one side, then the other [left then right])
+- swap search directions (look first on right side of path)
+                   (default is inward for counter-clockwise path)
+- first jump away from search direction then search (assumes 4)
+          VAL  edge intensity value (default current Thresh value, or 1 if Thresh==0)
+,3,flg,dist h	 clean up nodes in path
+          FLG  1 - reuse same ROI (default is create new ROI)
+               ? - remove non-edge nodes (after 10,2h cmd)
+- remove kinks (where path doubles back on itself)
+- remove outliers (where path jumps
+- smooth regardless of distance (default: smooth small jumps)
+          DIST
+,5,flg,val,plane h     Generate contour ROI for image mask(s)
+               This creates a contour around the border of the image
+               region with intensity VAL (each value >0 by default)
+               Note: this is inverse of 9h cmd.
           FLG  1 - inside voxels have values >= VAL (default)
 - inside voxels have values <= VAL
@@ Line 159: / Line 180: @@
 - edge is intensity increase >= VAL %
           VAL  edge intensity value (default current Thresh value, or 1 if Thresh==0)
-,3,flg h       discard NO_EDGE nodes in path
+          PLANE is 0,1,2 for which image plane x,y,z to draw contours
-,5,flg,val,plane h
+               (plane=2, z, by default.
-                        Generate contour ROI for image mask(s)
-                        This creates a contour around the border of the image
-                        region with intensity VAL (each value >0 by default)
-          PLANE is 0,1,2 for which image plane x,y,z to draw contours (plane=2, z, by default.
-	  Note: this is inverse of 9h cmd.
 h                Sample values in a region (ROI or near cursor)
      'name',11,flg,roinum,dist,thresh h