antsrVol | R Documentation |
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.
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
)
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 |
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 |
no output
Avants BB, Tustison NJ
## 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)
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