antsrSurf: Render a function onto a surface.

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

Render a function onto a surface.

Description

Use a system call to antsSurf in order to render a function onto a surface. This requires antsSurf to be in the environment as well as ConvertScalarImageToRGB, both available in Advanced Normalization Tools software on github.

Usage

antsrSurf(
  x,
  y,
  z,
  quantlimits = c(0.1, 0.9),
  colormap = "jet",
  alpha = NA,
  inflationFactor = 25,
  smoothingSigma = 0,
  rotationParams = c(270, 0, 270),
  overlayLimits = NA,
  backgroundColor,
  filename = NA,
  antspath = NA,
  verbose = FALSE
)

Arguments

x	input antsImage defining the surface on which to render
y	input antsImage list defining the function to render on the surface. these image(s) should be in the same space as x.
z	input antsImage list mask for each y function to render on the surface. these image(s) should be in the same space as y.
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
alpha	transparency vector for underlay and each overlay, default zero
inflationFactor	number of inflation iterations to run
smoothingSigma	gaussian smooth the overlay by this sigma
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]. Can be a list of length of y.
backgroundColor	a three entry vector where each entry is in the range of 0 to 255 and corresponds to red green and blue color channels. Alternatively, pass a string white or black.
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 antsSurf

Value

no output

Author(s)

Avants BB, Tustison NJ

Examples

## Not run: 

myantspath <- Sys.getenv("ANTSPATH")
surf_ex <- file.path(myantspath, "antsSurf")
if (file.exists(surf_ex)) {
  ch2i <- antsImageRead(getANTsRData("ch2"))
  ch2seg <- thresholdImage(ch2i, "Otsu", 3)
  wm <- thresholdImage(ch2seg, 3, 3)
  wm2 <- smoothImage(wm, 1) %>% thresholdImage(0.5, Inf)
  kimg <- weingartenImageCurvature(ch2i, 1.5) %>% smoothImage(1)
  rp1 <- matrix(c(90, 180, 90), ncol = 3)
  rp2 <- matrix(c(90, 180, 270), ncol = 3)
  rp3 <- matrix(c(90, 180, 180), ncol = 3)
  rp <- rbind(rp1, rp3, rp2)
  antsrSurf(
    x = wm2, y = list(kimg), z = list(wm2 %>% iMath("MD", 3)),
    inflationFactor = 255, overlayLimits = c(-0.3, 0.3), verbose = TRUE,
    rotationParams = rp, filename = tempfile()
  )

  fn <- getANTsRData("surf")
  img <- antsImageRead(fn) # see antsSurf on github for data
  wm <- thresholdImage(img, 3, 4)
  wm <- thresholdImage(img, 3, 4) %>% iMath("FillHoles")
  wm <- wm %>% thresholdImage(1, 2)
  wms <- smoothImage(wm, 1.0)
  wmk <- weingartenImageCurvature(wms, 1.5, 0)
  # will display to screen
  antsrSurf(
    x = wm, y = list(wmk %>% smoothImage(1)), z = list(wm %>% iMath("MD", 1)),
    rotationParams = c(270, 0, 90), overlayLimits = c(-0.4, 0.4)
  )
  # surface and two overlays
  blob <- antsImageRead(getANTsRData("blob"))
  blob[1:266, 1:266, 1:100] <- 0
  z <- list(wm %>% iMath("MD", 1), blob %>% smoothImage(1))
  antsrSurf(
    x = wm, y = list(wmk %>% smoothImage(1), blob), z = z,
    colormap = c("jet", "blue"), alpha = c(1, 0.5, 1),
    rotationParams = c(270, 0, 90),
    overlayLimits = list(c(-0.4, 0.4), c(0.9, 1.001))
  )
  # separate pos and neg curvature
  y <- list(
    thresholdImage(wmk, 0.00, Inf),
    thresholdImage(wmk, -100, -0.00)
  )
  z <- list(
    y[[1]] %>% iMath("MD", 1),
    y[[2]] %>% iMath("MD", 1)
  )
  antsrSurf(
    x = wm, y = y, z = z, smoothingSigma = 0.5, alpha = c(1, 1, 1),
    colormap = c("red", "blue"),
    inflationFactor = 155, overlayLimits = list(c(0.5, 1.0001), c(0.5, 1.0001)),
    verbose = TRUE, rotationParams = rp[1, ]
  )
}

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.