Approximate 'sub-cortical' surfaces from 'parcellation' — generate_subcortical

Superseded by volume_to_surf. Please do not use this function.

Usage

generate_subcortical_surface(
  atlas,
  index,
  save_prefix = NULL,
  label = NULL,
  IJK2RAS = NULL,
  grow = 1,
  remesh = TRUE,
  smooth = TRUE,
  smooth_delta = 3,
  ...
)

Arguments

atlas: path to imaging 'parcellation', can be 'nii' or 'mgz' formats
index: 'parcellation' index, see 'FreeSurfer' look-up table
save_prefix: parent folder to save the resulting surface
label: character label or name of the 'sub-cortical' structure, usually automatically derived from index
IJK2RAS: an 'Affine' matrix from 'voxel' index to 'tkrRAS', usually automatically derived from atlas
grow: amount to grow (dilate) before generating mesh
remesh, smooth, smooth_delta, ...: passed to mesh_from_volume

Value

A surface mesh, containing 'atlas' index, label, surface nodes and face indices.