Make ggseg atlas from volumetric template

Source: R/create-ggseg-atlas.R

If making an atlas from a non-cortical atlas, volumetric atlases are the best options. Instead of snapshotting images of inflated brain, will snapshot brain slices given x, y, z coordinates for the slices trhoush the slices argument.

make_volumetric_ggseg(
  label_file,
  subject = "fsaverage5",
  subjects_dir = fs_subj_dir(),
  output_dir = tempdir(),
  color_lut = NULL,
  steps = 1:8,
  skip_existing = TRUE,
  slices = data.frame(x = c(130, 122, 122), y = c(130, 235, 112), z = c(130, 100, 106),
    view = c("axial", "sagittal", "coronal"), stringsAsFactors = FALSE),
  vertex_size_limits = NULL,
  dilate = NULL,
  tolerance = 0,
  ncores = 2,
  smoothness = 5,
  verbose = TRUE,
  cleanup = FALSE
)

Arguments

label_file

a volumetric image containing the labels
subject

Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
subjects_dir

Freesurfer subject directory
output_dir

output directory path
color_lut

a file containing color information for the labels
steps

numeric vector of steps to run
skip_existing

logical. If slice snapshots already exist, should these be skipped.
slices

a data.frame with columns x, y, z, and view specifying coordinates and view of slice snapshots.
vertex_size_limits

numeric vector of two, setting the minimum and maximum vector size of polygons. Defaults to NULL, which sets no limits.
dilate

numeric. Dilation factor for polygons. Default NULL applies no dilation.
tolerance

tolerance during vertex reduction st_simplify
ncores

number of cores for parallel processing (default numcores-2)
smoothness

smoothing factor, argument to smooth
verbose

logical indicating to be verbose or not
cleanup

logical to toggle removal of all intermediary files

Value

brain-atlas class

Examples

if (FALSE) {

   label_file <- file.path(fs_subj_dir(), subject, "mri/aseg.mgz")
   slices = data.frame(x=130, y=130, z=130, view="axial", stringsAsFactors = FALSE)
   
   aseg2 <- make_volumetric_ggseg(
      label_file =  label_file,
      slices = slices
   )

   # Have a look at the atlas
   plot(aseg2)
}