make_aparc_2_3datlas: Create cortical ggseg3d-atlas from annot-file

In neuroconductor/ggsegExtra: Extra Utilities for the 'ggseg'-Plotting Tool

Description

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

Usage

make_aparc_2_3datlas(
  annot = "aparc",
  subject = "fsaverage5",
  hemisphere = c("rh", "lh"),
  surface = c("inflated", "LCBC", "white"),
  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

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.

Value

nested data frame as ggseg3d-atlas

Examples

## Not run: 
dt <- aparc_2_3datlas()
dt <- aparc_2_3datlas(annot = "aparc.a2009s")
dt <- aparc_2_3datlas(surface = "sphere")

## End(Not run)

neuroconductor/ggsegExtra documentation built on Aug. 18, 2020, 4:45 p.m.