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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(), tracula()

Examples

aseg()
#> 
#> ── aseg ggseg atlas ────────────────────────────────────────────────────────────
#> Type: subcortical
#> Regions: 19
#> Hemispheres: left, NA, right
#> Views: axial_3, axial_4, axial_5, axial_6, coronal_1, coronal_2, sagittal
#> Palette: ✔
#> Rendering: ✔ ggseg
#> ✔ ggseg3d (meshes)
#> ────────────────────────────────────────────────────────────────────────────────
#> # A tibble: 47 × 4
#>    hemi  region           label                   structure    
#>    <chr> <chr>            <chr>                   <chr>        
#>  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
#> 11 left  Pallidum         Left-Pallidum           basal ganglia
#> 12 left  Pallidum         Left-Pallidum           basal ganglia
#> 13 NA    Brain Stem       Brain-Stem              brainstem    
#> 14 left  Hippocampus      Left-Hippocampus        limbic       
#> 15 left  Hippocampus      Left-Hippocampus        limbic       
#> 16 left  Amygdala         Left-Amygdala           limbic       
#> 17 left  Amygdala         Left-Amygdala           limbic       
#> 18 left  accumbens area   Left-Accumbens-area     NA           
#> 19 left  ventraldc        Left-VentralDC          NA           
#> 20 left  vessel           Left-vessel             NA           
#> 21 left  choroid plexus   Left-choroid-plexus     NA           
#> 22 right Cerebellum       Right-Cerebellum-Cortex cerebellum   
#> 23 right Cerebellum       Right-Cerebellum-Cortex cerebellum   
#> 24 right Thalamus         Right-Thalamus          basal ganglia
#> 25 right Thalamus         Right-Thalamus          basal ganglia
#> 26 right Thalamus Proper  Right-Thalamus          basal ganglia
#> 27 right Thalamus Proper  Right-Thalamus          basal ganglia
#> 28 right Caudate          Right-Caudate           basal ganglia
#> 29 right Caudate          Right-Caudate           basal ganglia
#> 30 right Putamen          Right-Putamen           basal ganglia
#> 31 right Putamen          Right-Putamen           basal ganglia
#> 32 right Pallidum         Right-Pallidum          basal ganglia
#> 33 right Pallidum         Right-Pallidum          basal ganglia
#> 34 right Hippocampus      Right-Hippocampus       limbic       
#> 35 right Hippocampus      Right-Hippocampus       limbic       
#> 36 right Amygdala         Right-Amygdala          limbic       
#> 37 right Amygdala         Right-Amygdala          limbic       
#> 38 right accumbens area   Right-Accumbens-area    NA           
#> 39 right ventraldc        Right-VentralDC         NA           
#> 40 right vessel           Right-vessel            NA           
#> 41 right choroid plexus   Right-choroid-plexus    NA           
#> 42 NA    Optic Chiasm     Optic-Chiasm            other        
#> 43 NA    cc posterior     CC_Posterior            NA           
#> 44 NA    cc mid posterior CC_Mid_Posterior        NA           
#> 45 NA    cc central       CC_Central              NA           
#> 46 NA    cc mid anterior  CC_Mid_Anterior         NA           
#> 47 NA    cc anterior      CC_Anterior             NA           

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"