Create cortical ggseg3d-atlas from annot-file

Source: R/create-ggseg3d-atlas.R

Function loops through hemispheres and surfaces to create a data frame that is ready to use with ggseg3d.

make_aparc_2_3datlas(
  annot,
  subject = "fsaverage5",
  hemisphere = c("rh", "lh"),
  surface = c("inflated", "LCBC"),
  subjects_dir = freesurfer::fs_subj_dir(),
  annot_dir = file.path(subjects_dir, subject, "label"),
  output_dir = tempdir(),
  ncores = parallel::detectCores() - 2,
  cleanup = TRUE,
  verbose = TRUE
)

Arguments

annot

annotation file, with name [hemi].[annot].annot abd be in annot_dir
subject

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

hemisphere, either "rh" or "lh"
surface

Freesurfer surface
subjects_dir

Freesurfer subject directory
annot_dir

path to directory with annot-files
output_dir

output directory path
ncores

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

logical to toggle removal of all intermediary files
verbose

logical indicating to be verbose or not

Value

nested data frame as ggseg3d-atlas

Details

It is recommended that you change the region names for the atlas, and the atlas name to something shorter. See the dk_3d atlas for examples.

Examples

if (FALSE) {
dt <- aparc_2_3datlas(annot = "aparc.a2009s")
dt <- aparc_2_3datlas(annot = "aparc.a2009s",
                      surface = "sphere")
}