antsrVol: Render an image volume with or without overlay.

In neuroconductor/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Description

Use a system call to antsVol in order to render an image. This requires antsVol to be in the environment as well as ConvertScalarImageToRGB, both available in Advanced Normalization Tools software on github.

Usage

antsrVol(
  x,
  y,
  quantlimits = c(0.1, 0.9),
  colormap = "jet",
  rotationParams = c(270, 0, 270),
  overlayLimits = NA,
  magnificationFactor = 1,
  intensityTruncation = c(0, 1),
  filename = NA,
  antspath = NA,
  verbose = FALSE
)

Arguments

x	input antsImage defining the image to render
y	input antsImage list defining the function to render on the image. these image(s) should be in the same space.
quantlimits	lower and upper quantile limits for overlay
colormap	character, one of: grey, red, green, blue, copper, jet, hsv, spring, summer, autumn, winter, hot, cool, overunder, custom
rotationParams	3 Rotation angles expressed in degrees or a matrix of rotation parameters that will be applied in sequence.
overlayLimits	absolute lower and upper limits for functional overlay. this parameter will override quantlimits. Currently, this will set levels above overlayLimits[2] to overlayLimits[2].
magnificationFactor	zooms in on image during rendering
intensityTruncation	lower and upper quantiles at which to truncate intensity
filename	prefix filename for output pngs
antspath	pass the ANTSPATH here otherwise we try to detect it from environment
verbose	prints the command used to call antsVol

Value

no output

Author(s)

Avants BB, Tustison NJ

Examples

## Not run: 
ch2i = antsImageRead( getANTsRData("mni") )
ch2seg = thresholdImage( ch2i, "Otsu", 3 )
wm   = thresholdImage( ch2seg, 3, 3 )
kimg = weingartenImageCurvature( ch2i, 1.5  ) %>% smoothImage( 1 )
ap = path.expand( "~/code/ants-src/bin/" )
rp0 = matrix( c(90,180,90), ncol = 3 )
rp2 = matrix( c(0,0,0), ncol = 3 )
rp3 = matrix( c(270,90,90), ncol = 3 )
rp  = rbind( rp0, rp2, rp3 ) # pass these as rotationParams
antsrVol( wm, list( kimg ), quantlimits=c(0.01,0.99) )

## End(Not run)

neuroconductor/ANTsR documentation built on Oct. 11, 2020, 8:14 a.m.