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FreeSurfer Automatic Subcortical Segmentation Atlas

Source: R/atlases.R
aseg.Rd

Returns the FreeSurfer automatic subcortical segmentation (aseg) atlas containing deep brain structures including the thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, and ventricles.

Usage

aseg()

Value

A ggseg_atlas object with components:

atlas

Character. Atlas name ("aseg")

type

Character. Atlas type ("subcortical")

palette

Named character vector of colours for each region

data

A ggseg_data_subcortical object containing:

meshes

Data frame with label and mesh columns

sf

Simple features data frame for 2D rendering

Details

This atlas is derived from FreeSurfer's aseg.mgz volumetric segmentation. It works with both ggseg (2D slice views) and ggseg3d (3D mesh visualizations) from a single object.

Structures

The atlas contains bilateral structures:

  • Thalamus

  • Caudate

  • Putamen

  • Pallidum (globus pallidus)

  • Hippocampus

  • Amygdala

  • Accumbens (nucleus accumbens)

  • Ventral diencephalon

Plus midline and ventricular structures:

  • Lateral ventricles

  • Third ventricle

  • Fourth ventricle

  • Brain stem

  • Cerebellar cortex

  • Cerebellar white matter

References

Fischl B, Salat DH, Busa E, et al. (2002). Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3):341-355. doi:10.1016/S0896-6273(02)00569-X

See also

dk() for cortical parcellation, ggseg_atlas() for the atlas class constructor

Other ggseg_atlases: dk(), suit(), tracula()

Examples

aseg()
#> 
#> ── aseg ggseg atlas ────────────────────────────────────────────────────────────
#> Type: subcortical
#> Regions: 18
#> Hemispheres: left, NA, right
#> Views: axial_3, axial_4, axial_5, axial_6, coronal_1, coronal_2, sagittal
#> Palette: ✔
#> Rendering: ✔ ggseg
#> ✔ ggseg3d (meshes)
#> ────────────────────────────────────────────────────────────────────────────────
#>    hemi            region                  label                names
#> 1  left cerebellum cortex Left-Cerebellum-Cortex    cerebellum cortex
#> 2  left          thalamus          Left-Thalamus             thalamus
#> 3  left           caudate           Left-Caudate              caudate
#> 4  left           putamen           Left-Putamen              putamen
#> 5  left          pallidum          Left-Pallidum             pallidum
#> 6  <NA>        brain stem             Brain-Stem           brain stem
#> 7  left       hippocampus       Left-Hippocampus          hippocampus
#> 8  left          amygdala          Left-Amygdala             amygdala
#> 9  left    accumbens area    Left-Accumbens-area            accumbens
#> 10 left         ventraldc         Left-VentralDC ventral diencephalon
#>        structure
#> 1     cerebellum
#> 2  basal ganglia
#> 3  basal ganglia
#> 4  basal ganglia
#> 5  basal ganglia
#> 6      brainstem
#> 7         limbic
#> 8         limbic
#> 9  basal ganglia
#> 10  diencephalon
#> ... with 19 more rows
plot(aseg())

atlas_regions(aseg())
#>  [1] "accumbens area"    "amygdala"          "brain stem"       
#>  [4] "caudate"           "cc anterior"       "cc central"       
#>  [7] "cc mid anterior"   "cc mid posterior"  "cc posterior"     
#> [10] "cerebellum cortex" "choroid plexus"    "hippocampus"      
#> [13] "optic chiasm"      "pallidum"          "putamen"          
#> [16] "thalamus"          "ventraldc"         "vessel"