write4D: Wrapper to write a 4D scene

In muschellij2/brainR: Helper Functions to 'misc3d' and 'rgl' Packages for Brain Imaging

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

scene	list of 3D triangles (see contour3d). If a multicolored object is to be rendered (multiple contours with one control) - it must be in a list
outfile	html filename that is to be exported
fnames	filenames for the 3D surfaces in the scene - needs to be the same length as scene
captions	labels for checkboxes on html webpage
writefiles	(experimental) simply run the code to create the html and not write the .obj or .stl files
reprint	(logical, experimental) do you want to reprint the rgl before saving (common use by rgl functions)
...	other options to be passed to write4D.file

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)

muschellij2/brainR documentation built on April 1, 2021, 11 a.m.