Binary Objects

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Binary objects are volumes whose voxel values are either TRUE, FALSE or NA (i.e. undetermined). They act as a mask, and are used to select only the desired part of a volume.

The example below show how to select the brain voxels described in the rtstruct object.

nesting.MR <- nesting.roi (MR, S, roi.sname = "brain", T.MAT = pat$T.MAT, vol.restrict = TRUE, 
                           xyz.margin = c(20, 20, 20)) # to reduce the computation time 
bin.brain <- bin.from.roi (nesting.MR, struct = S, roi.sname = "brain", T.MAT = pat$T.MAT)
MR.brain <- vol.from.bin (nesting.MR, bin.brain)

The bin.from.vol function creates binary volumes by selecting voxels that are inside or outside an interval [min, max]. The example below selects voxels with a value greater than 150.

bin.min.150 <- bin.from.vol (MR.brain, min = 150)

display.plane (bin.min.150, view.coord = 0, view.type = "sagi", main = "bin.min.150",
               bg = "#379DA2", legend.plot = FALSE, sat.transp = TRUE, interpolate = TRUE)

The usual functions on binary volumes, such as inversion (bin.inversion), intersection (bin.intersection), union (bin.sum) and subtraction (bin.subtraction), have been implemented in the espadon package.

Other image processing functions are available:

bin.erosion decreases the volume of a radius r
bin.dilation increases the volume of a radius r
bin.closing is usefull for filling holes that are smaller than the radius and merging two shapes close to each other.
bin.opening is usefull for removing volumes that are smaller than the radius and smoothing shapes.
bin.clustering groups and labels TRUE voxels that have a 6-connectivity (i.e. sharing a common side).

These functions can be used to separate multiple volumes in the binary selection, as shown below:

bin.smooth <- bin.opening (bin.min.150, radius = 1.5))
bin.cluster <- bin.clustering (bin.smooth)

# Creation of ventricle contours
bin.ventricle <- bin.from.vol (bin.cluster, min = 1, max = 1)
S.ventricle <- struct.from.bin (bin.ventricle , roi.name = "ventricle", roi.color = "#FF0000" )

# Display of the first 3 largest sub-volumes, and ventricle contours
library (rgl)
bg3d ("black")
par3d (userMatrix = matrix (c(0, 0, -1, 0, -1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1), ncol = 4), 
       windowRect = c(0, 50, 300, 300), zoom = 0.7)
display.3D.stack(bin.cluster, k.idx = bin.cluster$k.idx, col = c ("#00000000", rainbow (3, alpha = 1)), 
                 breaks = seq (0, 3, length.out = 5), border = FALSE, ktext = FALSE)
play3d (spin3d (rpm = 4), duration = 15)

bg3d ("black")
par3d (userMatrix = matrix (c(0, 0, -1, 0, -1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1), ncol = 4), 
       windowRect = c(0, 50, 300, 300), zoom = 1)
display.3D.contour (S.ventricle)
play3d (spin3d (rpm = 4), duration = 15)