# Creation of a binary volume according to RoI The `bin.from.roi` function creates a "volume" class object, of modality "binary" or "weight", by selecting the voxels defined by the RoI. ```r bin.from.roi( vol, struct, roi.name = NULL, roi.sname = NULL, roi.idx = NULL, T.MAT = NULL, within = TRUE, alias = "", description = NULL, modality = c("binary", "weight"), ... ) ``` ## Arguments - `vol`: "volume" class object. - `struct`: "struct" class object. - `roi.name`: Vector of exact names of the RoI in the `struct` object. By default `roi.name = NULL`. See Details. - `roi.sname`: Vector of names or parts of names of the RoI in the `struct` object. By default `roi.sname = NULL`. See Details. - `roi.idx`: Vector of indices of the RoI that belong to the `struct` object. By default `roi.idx = NULL`. See Details. - `T.MAT`: "t.mat" class object, created by load.patient.from.Rdcm or load.T.MAT . If `T.MAT = NULL`, `struct$ref.pseudo` must be equal to `vol$ref.pseudo`. - `within`: Boolean, defaults to `TRUE`. If `within = TRUE`, the contours included in a RoI are managed, depending on their `$level` field. If `within = FALSE`, only the `$level = 0` fields of the RoI are used (i.e. only the external outlines). - `alias`: Character string, `$alias` of the created object. - `description`: Character string, describing the created object. If `description = NULL` (default value), it will be set to `struct$roi.info$roi.pseudo[roi.idx]`. - `modality`: modality ("binary" or "weight") of the generated object. - `...`: additional argument. ## Returns Returns a "volume" class object of "binary" or "weight" modality (see espadon.class for class definitions), with the same grid as `vol`. * In the “binary” modality, voxels with 50 percent of their volume within the ROI are set to `TRUE`. * In the “weight” modality, the value of each voxel is its volume fraction included in the ROI. ## Details `roi.name`, `roi.sname`, and `roi.idx` must select only one RoI. ## Examples ```r # loading of toy-patient objects (decrease dxyz for better result) step <- 5 patient <- toy.load.patient (modality = c("ct", "rtstruct"), roi.name = c("eye", "optical nerve", "brain"), dxyz = rep (step, 3)) CT <- patient$ct[[1]] S <- patient$rtstruct[[1]] # "optical nerve" binary, with modality "binary" and "weight" binl <- bin.from.roi (CT, struct = S, roi.sname = "left optical", alias = "left_optical_nerve", verbose = FALSE, modality = "binary") binr <- bin.from.roi (CT, struct = S, roi.sname = "right optical", alias = "right_optical_nerve", verbose = FALSE, modality = "weight") view.coord <- S$roi.info[S$roi.info$roi.pseudo == "leftopticalnerve",]$Gz palette <- grey.colors(100, start = 0, end = 1, alpha = c(0, rep(1,99))) plot(S, view.coord = view.coord, main ="optical nerves") plot(binl, view.coord = view.coord, col = palette, cut.interpolate = FALSE, add = TRUE) plot(binr, view.coord = view.coord, col =palette, cut.interpolate = FALSE, add = TRUE) plot(S, view.coord = view.coord, lwd = 2, add= TRUE) ## Not run: # with a smaller step step <- 1 patient <- toy.load.patient (modality = c("ct", "rtstruct"), roi.name = c("eye", "optical nerve", "brain"), dxyz = rep (step, 3)) CT <- patient$ct[[1]] S <- patient$rtstruct[[1]] #' view.coord <- S$roi.info[S$roi.info$roi.pseudo == "leftopticalnerve",]$Gz # "optical nerve" binary without inclusions management bin <- bin.from.roi (CT, struct = S, roi.sname = "left optical", alias = "left_optical_nerve", within = FALSE, verbose = FALSE) display.plane (CT, top = bin, struct = S, view.coord = view.coord, legend.shift = -80, interpolate = FALSE, main = "Left nerve") # "optical nerve" binary with inclusions management bin <- bin.from.roi (CT, struct = S, roi.sname = "left optical", alias = "left_optical_nerve", within = TRUE, verbose = FALSE) display.plane (CT, top = bin, struct = S, view.coord = view.coord, legend.shift = -80, interpolate = FALSE, main = "Left nerve") ## End(Not run) ``` ## See Also bin.from.vol .

bin.from.roi function