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Introduction to ggseg.meshes

Source: vignettes/ggseg-meshes.Rmd
ggseg-meshes.Rmd

The ggseg ecosystem uses brain surface meshes to render atlas parcellations in 3D. The core packages ship with the inflated cortical mesh (in ggseg.formats) and the SUIT 3D pial cerebellar mesh. ggseg.meshes extends this with additional surfaces for both cortical and cerebellar visualisation.

Available surfaces

Cortical

All cortical meshes are fsaverage5 resolution: 10,242 vertices and 20,480 triangular faces per hemisphere.

available_cortical_surfaces()
#> [1] "pial"          "white"         "midthickness"  "semi-inflated"
#> [5] "sphere"        "smoothwm"      "orig"
Surface Description Use case
pial Grey matter / CSF boundary Anatomically accurate rendering
white Grey / white matter boundary White matter surface visualisation
midthickness Midpoint of pial + white HCP-style analyses, functional data sampling
semi-inflated 35/65 blend of white + inflated Compromise between anatomical accuracy and visibility
sphere Spherical registration surface Surface-based registration, QC
smoothwm Smoothed white matter Smoother alternative to white surface
orig Pre-topology-correction surface Debugging surface reconstruction
pial white midthickness
pial white midthickness
semi-inflated sphere smoothwm
semi-inflated sphere smoothwm
orig
orig

Cerebellar 

available_cerebellar_surfaces()
#> [1] "suit_flat"

The SUIT flatmap is a 2D flattened projection of the cerebellar cortex with 28,935 vertices. Vertex indices from cerebellar atlases map directly to this surface since it shares the same vertex space as the SUIT 3D pial mesh in ggseg.formats (minus the 1,078 peduncular cap vertices).

SUIT cerebellar flatmap
SUIT cerebellar flatmap

Accessing meshes

Each mesh is a list with vertices (data.frame: x, y, z) and faces (data.frame: i, j, k).

mesh <- get_cortical_mesh("lh", "pial")
head(mesh$vertices)
#>              x         y         z
#> 1 -19.34336472 38.735958 67.220139
#> 2 -69.06122589 16.662487 61.281273
#> 3  -9.23326397  9.717618 46.580341
#> 4  43.11487198 24.019428 23.926214
#> 5   0.04929276 59.861500  8.974564
#> 6 -49.40507889 50.645546 47.813751
head(mesh$faces)
#>   i    j    k
#> 1 1 2565 2563
#> 2 1 2563 2566
#> 3 1 2566 2568
#> 4 1 2568 2570
#> 5 1 2570 2565
#> 6 4 2575 2573
flat <- get_cerebellar_flatmap()
nrow(flat$vertices)
#> [1] 28935
nrow(flat$faces)
#> [1] 56588

Integration with ggseg3d

When ggseg.meshes is installed, ggseg3d::resolve_brain_mesh() can resolve all surfaces provided by this package. This means you can render atlases on any surface:

library(ggseg3d)

ggseg3d(atlas = dk(), surface = "pial") |>
  pan_camera("left lateral")

ggseg3d(atlas = dk(), surface = "white") |>
  pan_camera("left lateral")

Mesh structure

All cortical meshes share the same face topology (triangle connectivity) as the inflated mesh in ggseg.formats. This means vertex indices from cortical atlases work with any surface – the same vertex index refers to the same anatomical location across pial, white, inflated, sphere, etc.

vapply(
  available_cortical_surfaces(),
  function(s) {
    mesh <- get_cortical_mesh("lh", s)
    c(vertices = nrow(mesh$vertices), faces = nrow(mesh$faces))
  },
  integer(2)
)
#>           pial white midthickness semi-inflated sphere smoothwm  orig
#> vertices 10242 10242        10242         10242  10242    10242 10242
#> faces    20480 20480        20480         20480  20480    20480 20480

The cerebellar flatmap shares vertex indices with the SUIT 3D pial mesh (indices 0–28,934), so cerebellar atlas vertex assignments apply to both the 3D and flatmap representations.