Methods for Function overlay

Methods for function overlay

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"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

overlay(x, y, ...)

# S4 method for nifti,missing
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"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

# S4 method for nifti,nifti
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"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

# S4 method for anlz,anlz
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"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

# S4 method for anlz,nifti
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"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

# S4 method for nifti,anlz
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"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

# S4 method for array,array
overlay(x, y, ...)

# S4 method for array,nifti
overlay(x, y, ...)

# S4 method for nifti,array
overlay(x, y, ...)

# S4 method for array,anlz
overlay(x, y, ...)

# S4 method for anlz,array
overlay(x, y, ...)

# S4 method for afni,afni
overlay(x, y, ...)

# S4 method for afni,array
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’).
plot.type	allows the choice between all slices being displayed, in a matrix (left-to-right, top-to-bottom), or a single slice.
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`
...	other arguments to the `image` function may be provided here.

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.

Methods

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

Author

Brandon Whitcher bwhitcher@gmail.com

Arguments

Details

Methods

See also

Author