ANTsR (version 0.4.0)

antsrVol: Render an image volume with or without overlay.

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

Examples

# NOT RUN {
# }
# 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) )
# }
# NOT RUN {
# }