ANTsR (version 0.7.2.0)

antsrSurf: 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

Examples

# NOT RUN {
# }
# 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")
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,] )
}
# }
# NOT RUN {
# }