rtists (R for Tissue Integrity Superimposed on Tractography Streamlines) provides interactive 3-D visualisation of tractography streamlines and bundles defined in the fiber package.

The main function is plot3d(), an S7 generic with methods for both fiber::streamline and fiber::bundle objects. Figures are rendered by plotly and are fully interactive (pan, rotate, zoom).

Install the development version from GitHub:

# install.packages("pak")
pak::pak("tractoverse/rtists")

library(rtists)
library(fiber)

pts <- matrix(
  c(
    0, 0, 0,
    1, 2, 1,
    2, 3, 3,
    3, 3, 5,
    4, 2, 6,
    5, 1, 7
  ),
  ncol = 3, byrow = TRUE,
  dimnames = list(NULL, c("X", "Y", "Z"))
)

sl <- streamline(
  points          = pts,
  point_data      = list(FA = c(0.25, 0.40, 0.65, 0.70, 0.55, 0.30)),
  streamline_data = list(mean_FA = 0.475)
)

set.seed(42)
bun <- bundle(lapply(seq_len(6), function(i) {
  noise <- matrix(rnorm(nrow(pts) * 3, sd = 0.2), ncol = 3)
  colnames(noise) <- c("X", "Y", "Z")
  streamline(
    points          = pts + noise,
    point_data      = list(FA = pmin(pmax(sl@point_data$FA + rnorm(6, sd = 0.05), 0), 1)),
    streamline_data = list(mean_FA = mean(sl@point_data$FA))
  )
}))

All the following examples only display a static figure, but the actual output of plot3d() is an interactive widget. You might want to run the code yourself to see the full effect or take a look at the vignette for interactive 3D examples.

Each point is coloured by the direction of the local tangent vector using the standard DTI convention (left–right = red, anterior–posterior = green, superior–inferior = blue):

plot3d(bun)

#> list()

Pass any key from @point_data to map a continuous scalar to a colour scale:

plot3d(bun, color = "FA", palette = "Viridis")

#> list()

Keys from @streamline_data are broadcast to all points of each streamline, giving every tract a single uniform colour:

plot3d(bun, color = "mean_FA", palette = "RdYlBu")

#> list()

Any CSS colour name or hex code colours all lines identically:

plot3d(bun, color = "steelblue", opacity = 0.7, linewidth = 3)

#> list()

Additional arguments (palette, linewidth, opacity, ...) are documented in ?plot3d.