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Get the FreeSurfer Subcortical Atlas (ASEG)

Source: R/aseg_subcort.R
get_aseg_atlas.Rd

Loads and returns the FreeSurfer subcortical segmentation (ASEG) atlas, which provides probabilistic labels for key subcortical structures in the brain. The atlas includes bilateral structures such as the thalamus, caudate, putamen, and limbic regions, as well as midline structures like the brainstem.

Usage

get_aseg_atlas(outspace = NULL)

Arguments

outspace

Optional NeuroSpace object specifying the desired output space for resampling the atlas. If NULL (default), returns the atlas in its native space.

Value

A list with classes 'aseg' and 'atlas' containing:

atlas

A NeuroVol object containing the 3D volume of atlas labels

cmap

A data frame with RGB color specifications for each region

ids

Integer vector of region IDs present in the atlas

labels

Character vector of anatomical labels corresponding to each ID

hemi

Character vector indicating hemisphere ('left', 'right', or NA) for each region

Details

The ASEG atlas is derived from FreeSurfer's automatic subcortical segmentation algorithm and has been transformed into standard space. Each voxel contains an integer ID corresponding to a specific anatomical structure. The atlas includes major subcortical structures for both hemispheres:

  • Bilateral deep gray structures (thalamus, caudate, putamen, pallidum)

  • Limbic structures (hippocampus, amygdala)

  • Ventral structures (nucleus accumbens, ventral diencephalon)

  • Midline structures (brainstem)

References

Fischl, B., et al. (2002). Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341-355.

See also

map_atlas for mapping values onto atlas regions get_roi for extracting specific regions of interest

Examples

if (FALSE) { # \dontrun{
# Load the atlas in native space
aseg <- get_aseg_atlas()

# View the available region labels
aseg$labels

# Get the unique region IDs
aseg$ids
} # }