Methods for Function `slice'

Source: R/slice.R

Produce “lightbox” layout of slices for nifti, anlz and afni objects.

slice(x, ...)

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

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

# S4 method for array
slice(x, ...)

# S4 method for afni
slice(x, ...)

Arguments

x

is an object of class nifti or similar.
...

other arguments to the image function may be provided here.
z

is the slice to be displayed (ignored when plot.type = "multiple").
w

is the time point to be displayed (4D arrays only).
col

is grayscale (by default).
plane

is the plane of acquisition to be displayed (choices are ‘axial’, ‘coronal’, ‘sagittal’).
zlim

is set to NULL by default and utilizes the internal image range.
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.
useRaster

if TRUE, a bitmap raster is used to plot the image instead of polygons. Passed to image

Details

Uses the S3 generic function slice, with medical-image friendly settings, to display nifti, anlz and afni class objects in a “lightbox” layout.

Methods

x = "ANY"

Generic function: see image.

x = "nifti"

Produce images for x.

x = "anlz"

Produce images for x.

x = "afni"

Produce images for x.

See also

orthographic-methods, image-methods

Author

Brandon Whitcher bwhitcher@gmail.com