slice_overlay-methods: Methods for Function slice_overlay

Description

Methods for function slice_overlay

Usage

slice_overlay.nifti(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = TRUE,
  useRaster = TRUE,
  ...
)
slice_overlay(x, y, ...)
# S4 method for nifti,missing
slice_overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = TRUE,
  useRaster = TRUE,
  ...
)
# S4 method for nifti,nifti
slice_overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = TRUE,
  useRaster = TRUE,
  ...
)
# S4 method for anlz,anlz
slice_overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = TRUE,
  useRaster = TRUE,
  ...
)
# S4 method for anlz,nifti
slice_overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = TRUE,
  useRaster = TRUE,
  ...
)
# S4 method for nifti,anlz
slice_overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = TRUE,
  useRaster = TRUE,
  ...
)
# S4 method for array,array
slice_overlay(x, y, ...)
# S4 method for array,nifti
slice_overlay(x, y, ...)
# S4 method for nifti,array
slice_overlay(x, y, ...)
# S4 method for array,anlz
slice_overlay(x, y, ...)
# S4 method for anlz,array
slice_overlay(x, y, ...)
# S4 method for afni,afni
slice_overlay(x, y, ...)
# S4 method for afni,array
slice_overlay(x, y, ...)

Arguments

x, y: is an object of class nifti or similar.
z: is the slice to be displayed (ignored when plot.type = "multiple").
w: is the time point to be displayed (4D arrays only).
col.x: is grayscale (by default).
col.y: is hotmetal (by default).
zlim.x, zlim.y: are set to NULL (by default) and taken from the header information.
plane: is the plane of acquisition to be displayed (choices are ‘axial’, ‘coronal’, ‘sagittal’).
xlab: is set to “” since all margins are set to zero.
ylab: is set to “” since all margins are set to zero.
axes: is set to FALSE since all margins are set to zero.
oma: is the size of the outer margins in the par function.
mar: is the number of lines of margin in the par function.
bg: is the background color in the par function.
NA.x: Set any values of 0 in x to NA
NA.y: Set any values of 0 in y to NA
useRaster: if TRUE, a bitmap raster is used to plot the image instead of polygons. Passed to image
...: other arguments to the image function may be provided here.

Methods

x = "nifti", y = "nifti": Produce slice_overlay of y on x.
x = "anlz", y = "anlz": Produce slice_overlay of y on x.
x = "afni", y = "afni": Produce slice_overlay of y on x.

Author

Brandon Whitcher bwhitcher@gmail.com

Details

The image command is used multiple times to simultaneously visualize one of the three orthogonal planes in two multidimensional arrays, one on top of the other, for medical imaging data.

Description

Usage

Arguments

Methods

Author

Details

See Also