slice-methods: Methods for Function 'slice'

In neuroconductor-releases/oro.nifti: Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output

Description

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

Usage

slice(x, ...)

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

## S4 method for signature '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.

Author(s)

Brandon Whitcher [e-mail]

See Also

orthographic-methods, image-methods

neuroconductor-releases/oro.nifti documentation built on Jan. 1, 2021, 11:40 a.m.