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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: 19
#> Hemispheres: left, NA, right
#> Views: axial_3, axial_4, axial_5, sagittal, axial_6, coronal_1, coronal_2
#> Palette: ✔
#> Rendering: ✔ ggseg
#> ✔ ggseg3d (meshes)
#> ────────────────────────────────────────────────────────────────────────────────
#>    hemi          region                  label     structure
#> 1  left      Cerebellum Left-Cerebellum-Cortex    cerebellum
#> 2  left      Cerebellum Left-Cerebellum-Cortex    cerebellum
#> 3  left        Thalamus          Left-Thalamus basal ganglia
#> 4  left        Thalamus          Left-Thalamus basal ganglia
#> 5  left Thalamus Proper          Left-Thalamus basal ganglia
#> 6  left Thalamus Proper          Left-Thalamus basal ganglia
#> 7  left         Caudate           Left-Caudate basal ganglia
#> 8  left         Caudate           Left-Caudate basal ganglia
#> 9  left         Putamen           Left-Putamen basal ganglia
#> 10 left         Putamen           Left-Putamen basal ganglia
#> ... with 37 more rows
plot(aseg())

atlas_regions(aseg())
#>  [1] "Amygdala"         "Brain Stem"       "Caudate"          "Cerebellum"      
#>  [5] "Hippocampus"      "Optic Chiasm"     "Pallidum"         "Putamen"         
#>  [9] "Thalamus"         "Thalamus Proper"  "accumbens area"   "cc anterior"     
#> [13] "cc central"       "cc mid anterior"  "cc mid posterior" "cc posterior"    
#> [17] "choroid plexus"   "ventraldc"        "vessel"