misc3d (version 0.9-1)

slices3d: Interactive Image Slices of 3D or 4D Volume Data

Description

Uses tkrplot to create an interactive slice view of three or four dimensional volume data.

Usage

slices3d(vol1, vol2=NULL, rlim1, rlim2, col1, col2, main,
         scale = 0.8, alpha=1, cross = TRUE,
         layout=c("counterclockwise", "clockwise"))

Arguments

vol1

a three or four dimensional real array. If two images are overlaid, then this is the one at bottom.

vol2

a three or four dimensional real array. If two images are overlaid, then this is the one on top. The default value is NULL, when only vol1 is drawn.

rlim1

the minimum and maximum vol1 values for which colors should be plotted, defaulting to the range of the values of vol1.

rlim2

the minimum and maximum vol2 values for which colors should be plotted, defaulting to the range of the values of vol2, if two images are overlaid.

col1

a list of colors for vol1.

col2

a list of colors for vol2.

main

a character vector; main title for the plot.

scale

real value for scaling embedded plot size.

alpha

real value for transparency level, if two images are overlaid. The default value is 1.

cross

logical; if TRUE, show cross hairs of current slices.

layout

a character string specifying the layout. It must be either "counterclockwise" or "clockwise", and may be abbreviated. The default is "counterclockwise". Images corresponding to the x-y planes are always displayed in the third quadrant. If layout is counterclockwise, then the first quadrant shows images from the y-z planes and the second quadrant the x-z planes. Otherwise, the images in the first and the second quadrant are switched. The fourth quadrant is left for the slider used to select the value of the fourth index (if any) of input array(s).

Details

Shows slices of 3D array along the axes as produced by image, along with sliders for controlling which slices are shown. For 4D data an additional slider selects the value of the fourth index. Two images can be overlaid. This is useful for viewing medical imaging data (e.g. PET scans and fMRI data).

Examples

# NOT RUN {
  #Example 1: View of a mixture of three tri-variate normal densities
  nmix3 <- function(x, y, z, m, s) {
      0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
      0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
      0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
  }
  x<-seq(-2, 2, len=40)
  g<-expand.grid(x = x, y = x, z = x)
  v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
  slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))

# }
# NOT RUN {
  #Example 2: Put a z-map from fMRI data on top of a structure
  #           image. The threshold value of the z-map is 2.
  library(AnalyzeFMRI)
  temp<-f.read.analyze.volume("standard.img")
  z<-f.read.analyze.volume("z-map.img")
  slices3d(vol1=temp, vol2=z[,,,1], rlim2=c(2,Inf),col2=heat.colors(20),
          main="Regions above threshold values.")
  
# }