antsrVol.Rd
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.
input antsImage defining the image to render
input antsImage list defining the function to render on the image. these image(s) should be in the same space.
lower and upper quantile limits for overlay
character, one of: grey, red, green, blue, copper, jet, hsv, spring, summer, autumn, winter, hot, cool, overunder, custom
3 Rotation angles expressed in degrees or a matrix of rotation parameters that will be applied in sequence.
absolute lower and upper limits for functional overlay.
this parameter will override quantlimits
. Currently, this will set
levels above overlayLimits[2]
to overlayLimits[2]
.
zooms in on image during rendering
lower and upper quantiles at which to truncate intensity
prefix filename for output pngs
pass the ANTSPATH here otherwise we try to detect it from environment
prints the command used to call antsVol
no output
if (FALSE) { # \dontrun{
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))
} # }