Functions to render 3D brain images in html

Description

Brain Template from Copyright (C) 1993-2009 Louis Collins, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University 6th generation non-linear symmetric brain

Author(s)

John Muschelli muschellij2@gmail.com

References

G. Grabner, A. L. Janke, M. M. Budge, D. Smith, J. Pruessner, and D. L. Collins, "Symmetric atlasing and model based segmentation: an application to the hippocampus in older adults", Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv, vol. 9, pp. 58-66, 2006.

See Also

contour3d, rgl

Make Leveled Scene

Description

Make scene returns a list of levels - but makes them mutually distinct. So if cutoff 0.1, 0.2, then 0.1<= x < 0.2 is an roi, not > 0.1 and > 0.2. Different than contour3d as these are mutually exclusive levels.

Usage

makeScene(data, cutoffs, alpha, cols)

Arguments

Value

scene with multiple objects - can be passed to write4D

Wrapper to write a 4D scene

Description

This function takes in filenames, levels, and creates an output html file, with 4D elements. The html is based on XTK (https://github.com/xtk/X#readme)

Usage

scene4d(
  files,
  fnames = NULL,
  outfile = "index_4D_stl.html",
  levels = NULL,
  alpha = NULL,
  color = "white",
  useTemp = FALSE,
  MNITemp = c("1mm", "2mm"),
  objtype = "stl",
  ...
)

Arguments

Examples

### Faster - 8mm resampled but very coarse
imgs <- paste("Visit_", 1:5, "_8mm.nii.gz", sep="") 
ifiles <- sapply(imgs, system.file, package='brainR')
files = file.path(tempdir(), basename(ifiles))
file.copy(ifiles, files)
outfile <-  file.path(tempdir(), "index_4D_stl.html")
scene4d(files, levels=rep(0.99, length(files)), 
outfile = outfile, color= rep("blue", length(files)), useTemp=TRUE, 
MNITemp = "8mm", alpha = rep(1, length(files)), rescale=TRUE  )
## Not run: 
imgs <- paste("Visit_", 1:5, ".nii.gz", sep="") 
ifiles <- sapply(imgs, system.file, package='brainR')
files = file.path(tempdir(), basename(ifiles))
file.copy(ifiles, files)
scene4d(files, levels=rep(0.99, length(files)), 
outfile = outfile,
color= rep("blue", length(files)), useTemp=TRUEge, 
MNITemp = "8mm", alpha = rep(1, length(files)), rescale=TRUE  )

## End(Not run)

Wrapper to write a 4D scene

Description

This function takes in a scene and writes it out to a series of files either with the stl format or obj format (see writeOBJ and writeSTL)

Usage

write4D(
  scene,
  outfile,
  fnames = NULL,
  captions = NULL,
  writefiles = TRUE,
  reprint = TRUE,
  ...
)

Arguments

Examples

#Brain Template from Copyright (C) 1993-2009 Louis Collins,
#McConnell Brain Imaging Centre,
#Montreal Neurological Institute, McGill University
#6th generation non-linear symmetric brain
##Downsampled to 8mm using FSL fslmaths -subsamp2

template <- readNIfTI(system.file("MNI152_T1_8mm_brain.nii.gz", package="brainR")
, reorient=FALSE)
dtemp <- dim(template)
### 4500 - value that empirically value that presented a brain with gyri
### lower values result in a smoother surface
brain <- contour3d(template, x=1:dtemp[1], y=1:dtemp[2],
z=1:dtemp[3], level = 4500, alpha = 0.8, draw = FALSE)

### Example data courtesy of Daniel Reich
### Each visit is a binary mask of lesions in the brain
imgs <- paste("Visit_", 1:5, "_8mm.nii.gz", sep="")
files <- sapply(imgs, system.file, package='brainR')
scene <- list(brain)
## loop through images and thresh
nimgs <- length(imgs)
cols <- rainbow(nimgs)
for (iimg in 1:nimgs) {
mask <- readNIfTI(files[iimg], reorient=FALSE)
if (length(dim(mask)) > 3) mask <- mask[,,,1]
### use 0.99 for level of mask - binary
  activation <- contour3d(mask, level = c(0.99), alpha = 1,
  add = TRUE, color=cols[iimg], draw=FALSE)
## add these triangles to the list
scene <- c(scene, list(activation))
}
## make output image names from image names
fnames <- c("brain.stl", gsub(".nii.gz", ".stl", imgs, fixed=TRUE))
fnames = file.path(tempdir(), fnames)
outfile <-  file.path(tempdir(), "index.html")
write4D(scene=scene, fnames=fnames, outfile=outfile, standalone=TRUE, 
rescale=TRUE)
if (interactive()) {
if (requireNamespace("servr", quietly = TRUE)) {
   servr::httd(tempdir())
}
}
unlink(outfile)

Write a 4D scene

Description

This function takes in a scene and writes it out to a series of files either with the stl format or obj format

Usage

write4D.file(
  scene = NULL,
  outfile = "index_4D.html",
  fnames,
  visible = TRUE,
  opacity = 1,
  colors = NULL,
  captions = "",
  standalone = FALSE,
  rescale = FALSE,
  index.file = system.file("index_template.html", package = "brainR"),
  toggle = "checkbox",
  xtkgui = FALSE
)

Arguments

See Also

writeOBJ, writeSTL, contour3d

Examples

template <- readNIfTI(system.file("MNI152_T1_8mm_brain.nii.gz", package="brainR")
, reorient=FALSE)
dtemp <- dim(template)
### 4500 - value that empirically value that presented a brain with gyri
### lower values result in a smoother surface
brain <- contour3d(template, x=1:dtemp[1], y=1:dtemp[2],
z=1:dtemp[3], level = 4500, alpha = 0.8, draw = FALSE)

### Example data courtesy of Daniel Reich
### Each visit is a binary mask of lesions in the brain
imgs <- paste("Visit_", 1:5, "_8mm.nii.gz", sep="")
files <- sapply(imgs, system.file, package='brainR')
scene <- list(brain)
## loop through images and thresh
nimgs <- length(imgs)
cols <- rainbow(nimgs)
for (iimg in 1:nimgs) {
mask <- readNIfTI(files[iimg], reorient=FALSE)
if (length(dim(mask)) > 3) mask <- mask[,,,1]
### use 0.99 for level of mask - binary
  activation <- contour3d(mask, level = c(0.99), alpha = 1,
  add = TRUE, color=cols[iimg], draw=FALSE)
## add these triangles to the list
scene <- c(scene, list(activation))
}
## make output image names from image names
fnames <- c("brain.stl", gsub(".nii.gz", ".stl", imgs, fixed=TRUE))
fnames = file.path(tempdir(), fnames)
outfile <-  file.path(tempdir(), "index.html")
write4D.file(
scene=scene, fnames=fnames, 
visible = FALSE,
outfile=outfile, standalone=TRUE, rescale=TRUE)



unlink(outfile)
unlink(fnames)

Write STL triangles (without recalling the ids)

Description

This is code extracted from writeSTL in rgl. This allows users to write the triangles in STL without reprinting the rgl (which takes time)

Usage

writeTrianglesSTL(scene, con, ascii = FALSE)

Arguments

Value

filename (invisible) of stl object

Write WebGL with split triangles

Description

Adapted writeWebGL function that splits the triangles into 65535 vertices

Usage

writeWebGL_split(ids = rgl.ids()$id, writeIt = TRUE, verb = FALSE, ...)

Arguments

Value

if writeIt is TRUE, then returns the value from writeWebGL. Otherwise, returns the split triangles from the rgl objects

Examples

## Not run: 
#Brain Template from Copyright (C) 1993-2009 Louis Collins, 
#McConnell Brain Imaging Centre, 
#Montreal Neurological Institute, McGill University
#6th generation non-linear symmetric brain
template <- readNIfTI(system.file("MNI152_T1_2mm_brain.nii.gz", package="brainR")
, reorient=FALSE) 
dtemp <- dim(template)
### 4500 - value that empirically value that presented a brain with gyri
### lower values result in a smoother surface
brain <- contour3d(template, x=1:dtemp[1], y=1:dtemp[2], 
z=1:dtemp[3], level = 4500, alpha = 0.1, draw = FALSE)
drawScene.rgl(brain)
### this would be the ``activation'' or surface you want to render - 
# hyper-intense white matter
contour3d(template, level = c(8200, 8250), 
alpha = c(0.5, 0.8), add = TRUE, color=c("yellow", "red"))
### add text
text3d(x=dtemp[1]/2, y=dtemp[2]/2, z = dtemp[3]*0.98, text="Top")
text3d(x=-0.98, y=dtemp[2]/2, z = dtemp[3]/2, text="Right")
fname <- "knitted_webGL.html"
writeWebGL_split(dir=getwd(), filename =fname, 
template = system.file("my_template.html", package="brainR"), width=500, 
writeIt=TRUE)
browseURL(fname)

## End(Not run)