1 Econometrics, Business and Market Analysis Example(s)

# To Render the rgl/contour3d window in the DOCX/HTML output via knitter, we can use the following protocol:
library(misc3d)
library(rgl)
library(DT)

load("Fig3.11.Rdata")
dim(X1)

## [1]  64  64 180

dim(img1)

## [1] 64 64 91

# 1. download the 4D fMRI data
fMRIURL <- "http://socr.umich.edu/HTML5/BrainViewer/data/fMRI_FilteredData_4D.nii.gz"
fMRIFile <- file.path(tempdir(), "fMRI_FilteredData_4D.nii.gz")
(fMRIVolume <- readNIfTI(fMRIFile, reorient=FALSE))

# 2. extract the time-corse of 2D mid-axial slice (3D) hypervolume
fMRI_2D_z11 <- fMRIVolume[ , , 11, ]
X1 = fft(fMRI_2D_z11)

planes_half <- ceiling(dim(fMRI_2D_z11)[3]/2)
# apply log transform to temper the intensity range
img1 <- TCIU::fftshift(Re(log(1+X1)),3)[ , , (1:(planes_half+1))]

# Opening rgl window to display in html page
invisible(open3d(useNULL = T, windowRect = c(0,0,800,800), zoom = 1))
display1 <- 
  contour3d(img1, level = c(7, 12), alpha = c(0.3, 0.5), add = TRUE,
            color=c("yellow", "red"), perspective=T, distance=0.8)

# Aspect ratio and axes
aspect3d(1.0, 1.0, 1.0)
axes3d()

# Display scene
rglwidget(width = 800, height = 600, elementId = "model1") %>% 
  toggleWidget(ids = display1, label = "Show")