Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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 |
z |
input antsImage list mask for each |
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 |
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 |
no output
Avants BB, Tustison NJ
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | ## 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) )
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)
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