orthographic-methods {oro.nifti}R Documentation

Methods for Function ‘orthographic’ in Package ‘dcemriS4’

Description

Produce orthographic display for nifti, anlz and afni objects.

Usage

orthographic.nifti(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

orthographic(x, ...)

## S4 method for signature 'nifti'
orthographic(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

## S4 method for signature 'anlz'
orthographic(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

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

## S4 method for signature 'afni'
orthographic(x, ...)

Arguments

x

is an object of class nifti or similar.

y

is an object of class nifti or similar for the overlay.

xyz

is the coordinate for the center of the crosshairs.

w

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

col

is grayscale (by default).

col.y

is hotmetal (by default).

zlim

is the minimum and maximum ‘z’ values passed into image.

zlim.y

is the minimum and maximum ‘z’ values passed into image for the overlay.

crosshairs

is a logical value for the presence of crosshairs in all three orthogonal planes (default = TRUE).

col.crosshairs

is the color of the crosshairs (default = red).

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.

text

allows the user to specify text to appear in the fourth (unused) pane.

text.color

is the color of the user-specified text (default = “white”.

text.cex

is the size of the user-specified text (default = 2).

...

other arguments to the image function may be provided here.

Methods

x = "afni"

Produce orthographic display for x.

x = "anlz"

Produce orthographic display for x.

x = "array"

Produce orthographic display for x.

x = "nifti"

Produce orthographic display for x.

Author(s)

Brandon Whitcher bwhitcher@gmail.com

See Also

image-methods, overlay-methods

Examples

fname = system.file(
file.path("nifti", "mniRL.nii.gz"),
package = "oro.nifti")
eve = readNIfTI(fname)
orthographic(eve)

image(eve, z = 45)
image(eve, z = 45, plot.type = "single")
image(eve, z = c(45, 50), plot.type = "single")
[Package oro.nifti version 0.11.4 Index]