Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## 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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