ANTsR (version 0.3.3)

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, quantlimits = c(0.1, 0.9), colormap = "jet", inflationFactor = 25, rotationParams = c(270, 0, 270), overlayLimits = NA, 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 surf.

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

inflationFactor

number of inflation iterations to run

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].

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: 
# ch2i = antsImageRead( getANTsRData("mni") )
# ch2seg = thresholdImage( ch2i, "Otsu", 3 )
# wm   = thresholdImage( ch2seg, 3, 3 )
# wm2 = smoothImage( wm, 1 ) %>% thresholdImage( 0.2, 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( wm2, list( kimg ), inflationFactor=55, quantlimits=c(0.01,0.99),rotationParams = rp )
# 
# # show how to use absolute scales to allow comparison across renderings
# kimg = thresholdImage( ch2seg , 1, Inf )
# nvox = sum( ch2seg > 0 )
# voxvalsmat = cbind(
#     rnorm( nvox, 2.5, 2 ),
#     rnorm( nvox, 3.0, 2 ),
#     rnorm( nvox, 3.5, 2 ) )
# qq = quantile( voxvalsmat, 0.9 )
# for ( mmm in 1:3 )
# {
# kimg[ ch2seg > 0 ] = as.numeric(voxvalsmat[,mmm])
# kimg = smoothImage( kimg, 3 )
# antsrSurf( wm2, list( kimg ), inflationFactor=55, overlayLimits=c( 2.0, qq ),
#     rotationParams = rp, filename=paste('~/Downloads/ztempX',mmm,sep=''),
#     verbose=TRUE )
# }
# 
# fn = 'ADNI_137_S_0158_MR_MPR__GradWarp__N3__Scaled_Br_20070306171702344_S20209_I42985BrainSegmentation.nii.gz'
# img = antsImageRead( fn ) # see antsSurf on github for data
# wm   = thresholdImage( img, 3, 4 )
# # just the surface
# antsrSurf( x=wm, rotationParams = c(270, 0, 90) )
# # surface and one overlay
# wm = thresholdImage(img, 3, 4) %>% iMath("FillHoles")
# wms = smoothImage( wm, 1.0 )
# wmk = weingartenImageCurvature( wms, 1.5, 0 )
# antsrSurf( x=wm, y = list( wmk ), rotationParams = c(270, 0, 90), quantlimits=c(-0.5,0.5) )
# # surface and two overlays
# blob = antsImageRead( "manualBlob.nii.gz" ) %>% smoothImage( 1 )
# antsrSurf( x=wm, y = list( wmk, blob ), colormap=c("red","blue"),
#   rotationParams = c(270, 0, 90),  quantlimits=c(0.1,0.9))
# 
# ## End(Not run)