Additional Brain Surface Meshes for the ggsegverse Ecosystem • ggseg.meshes

Additional brain surface meshes for the ggsegverse ecosystem. Ships cortical and cerebellar surfaces beyond the inflated cortical and SUIT 3D pial meshes bundled with the core packages.

Meshes

Cortical (fsaverage5)

All cortical meshes are at fsaverage5 resolution (10,242 vertices, 20,480 faces per hemisphere).

Surface	Description
`pial`	Grey matter / CSF boundary
`white`	Grey / white matter boundary
`midthickness`	Midpoint of pial and white surfaces
`semi-inflated`	35/65 blend of white and inflated
`sphere`	Spherical registration surface
`smoothwm`	Smoothed white matter surface
`orig`	Original surface before topology correction

Cerebellar (SUIT)

Surface	Description
`suit_flat`	SUIT flatmap projection (28,935 vertices)

Installation

Install from the ggsegverse r-universe:

options(
  repos = c(
    ggsegverse = "https://ggsegverse.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
  )
)
install.packages("ggseg.meshes")

Or from GitHub:

# install.packages("remotes")
remotes::install_github("ggsegverse/ggseg.meshes")

Usage

library(ggseg.meshes)

mesh <- get_cortical_mesh("lh", "pial")
str(mesh)
#> List of 2
#>  $ vertices:'data.frame':    10242 obs. of  3 variables:
#>   ..$ x: num [1:10242] -19.3434 -69.0612 -9.2333 43.1149 0.0493 ...
#>   ..$ y: num [1:10242] 38.74 16.66 9.72 24.02 59.86 ...
#>   ..$ z: num [1:10242] 67.22 61.28 46.58 23.93 8.97 ...
#>  $ faces   :'data.frame':    20480 obs. of  3 variables:
#>   ..$ i: int [1:20480] 1 1 1 1 1 4 4 4 5 5 ...
#>   ..$ j: int [1:20480] 2565 2563 2566 2568 2570 2575 2573 2576 2582 2580 ...
#>   ..$ k: int [1:20480] 2563 2566 2568 2570 2565 2573 2576 2578 2580 2583 ...
#>  - attr(*, "face_index_base")= int 1

available_cortical_surfaces()
#> [1] "pial"          "white"         "midthickness"  "semi-inflated"
#> [5] "sphere"        "smoothwm"      "orig"
available_cerebellar_surfaces()
#> [1] "suit_flat"

With ggseg3d

ggseg.meshes integrates with ggseg3d through resolve_brain_mesh(). When installed, all surfaces become available for 3D rendering:

library(ggseg3d)

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

Citation

Mowinckel & Vidal-Piñeiro (2020). Visualization of Brain Statistics With R Packages ggseg and ggseg3d. Advances in Methods and Practices in Psychological Science. doi:10.1177/2515245920928009

Funding

This tool is partly funded by:

EU Horizon 2020 Grant: Healthy minds 0-100 years: Optimising the use of European brain imaging cohorts (Lifebrain).

Grant agreement number: 732592.

Call: Societal challenges: Health, demographic change and well-being