ggsegFreeSurfer

This package provides FreeSurfer cortical and subcortical brain atlases formatted for use with ggseg.

Installation

We recommend installing the ggseg-atlases through the ggseg r-universe:

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

install.packages("ggsegFreeSurfer")

You can install this package from GitHub with:

# install.packages("pak")
# pak::pak("ggsegverse/ggsegFreeSurfer")
install.packages("ggsegFreeSurfer", repos = c('https://ggsegverse.r-universe.dev', 'https://cloud.r-project.org'))

Cortical atlases

Desikan-Killiany-Tourville (DKT) atlas

library(ggseg)
library(ggsegFreeSurfer)

plot(dkt())

Destrieux atlas

plot(destrieux())

Subcortical atlases

The subcortical atlases are embedded in the full-brain aseg, so each slice view shows the structure of interest within its anatomical context (cerebral cortex and white matter rendered grey).

Anterior/posterior hippocampus atlas

plot(hcpa())

Thalamic nuclei atlas

plot(thalamus())

Hippocampal subfields & amygdala nuclei atlas

plot(hippoamyg())

Brainstem substructures atlas

plot(brainstem())

Hypothalamic subunits atlas

plot(hypothalamus())

Data source

Desikan RS, Segonne F, Fischl B, Quinn BT, Dickerson BC, Blacker D, … & Killiany RJ (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage, 31(3), 968-980.

Destrieux C, Fischl B, Dale A, & Halgren E (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53(1), 1-15.

Iglesias JE, Augustinack JC, Nguyen K, Player CM, Player A, Wright M, … & Van Leemput K (2015). A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI. NeuroImage, 115, 117-137.

Iglesias JE, Van Leemput K, Bhatt P, Casillas C, Dutt S, Schuff N, … & Fischl B (2015). Bayesian segmentation of brainstem structures in MRI. NeuroImage, 113, 184-195.

Saygin ZM, Kliemann D, Iglesias JE, van der Kouwe AJW, Boyd E, Reuter M, … & Fischl B (2017). High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas. NeuroImage, 155, 370-382.

Iglesias JE, Insausti R, Lerma-Usabiaga G, Bocchetta M, Van Leemput K, Greve DN, … & Paz-Alonso PM (2018). A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage, 183, 314-326.

Billot B, Bocchetta M, Todd E, Dalca AV, Rohrer JD, & Iglesias JE (2020). Automated segmentation of the hypothalamus and associated subunits in brain MRI. NeuroImage, 223, 117287.