The fiber package provides
three S7 classes — streamline,
bundle, and bundle_set — for representing diffusion MRI tractography
data in R, together with a concise set of methods:
A streamline stores:
-
@points— an$n \times 3$ numeric matrix with columns"X","Y","Z". -
@point_data— a named list of per-point vectors of length$n$ (any type). -
@streamline_data— a named list of per-streamline scalars (any type).
A bundle stores:
@streamlines— a list ofstreamlineobjects.@bundle_data— a named list of bundle-level metadata.
A bundle_set stores:
@bundles— a named list ofbundleobjects (names typically encode subject or session IDs, e.g."sub-01").@set_data— a named list of set-level metadata.
You can install the development version of fiber from GitHub with:
# install.packages("pak")
pak::pak("tractoverse/fiber")library(fiber)
# Build a helix streamline (50 points)
t <- seq(0, 2 * pi, length.out = 50)
sl <- streamline(
points = cbind(X = cos(t), Y = sin(t), Z = t / (2 * pi))
)
sl
#> <streamline [50 pts]>
# Shape descriptors
get_curvilinear_length(sl)
#> [1] 6.358015
get_sinuosity(sl)
#> [1] 6.358015
head(get_curvature(sl))
#> [1] 1.537338e-05 1.625127e-02 4.592627e-02 8.636675e-02 1.352354e-01
#> [6] 1.906608e-01
# Bundle two streamlines
sl2 <- streamline(
points = cbind(X = cos(t) * 1.1, Y = sin(t) * 1.1, Z = t / (2 * pi))
)
b <- bind_bundles(sl, sl2)
b
#> <bundle [2 streamlines | 50–50 pts/streamline]>
# Reparametrize to 20 points each
b20 <- reparametrize(b, n_points = 20L)
b20
#> <bundle [2 streamlines | 20–20 pts/streamline]>
# Hausdorff distance
compute_hausdorff_distance(sl, sl2)
#> [1] 0.1
# Multi-subject: collect bundles from two subjects into a bundle_set
b_sub01 <- bundle(
streamlines = list(sl),
bundle_data = list(subject = "sub-01")
)
b_sub02 <- bundle(
streamlines = list(sl2),
bundle_data = list(subject = "sub-02")
)
bs <- bind_bundle_sets("sub-01" = b_sub01, "sub-02" = b_sub02)
bs
#> <bundle_set [2 bundles | 1–1 streamlines/bundle]: sub-01, sub-02>
bs[["sub-01"]]
#> <bundle [1 streamlines | 50–50 pts/streamline] | bundle: subject>