make_aseg_2_3datlas: Subcortical segmentation to atlas

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

Description

Subcortical segmentation to atlas

Usage

make_aseg_2_3datlas(
  subject = "fsaverage5",
  subjects_dir = freesurfer::fs_subj_dir(),
  template = file.path(subjects_dir, subject, "mri/aseg.mgz"),
  color_lut = file.path(freesurfer::fs_dir(), "ASegStatsLUT.txt"),
  steps = 1:5,
  output_dir = tempdir(),
  verbose = TRUE,
  cleanup = TRUE
)

Arguments

subject	Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
subjects_dir	Freesurfer subject directory
template	tempalte volume.mgz file path
color_lut	Freesurfer colour look-up-table. Either as a path or a data.frame that is_ctab
steps	if cleanup is disabled, all files are saved, and steps can be re-run individually
output_dir	output directory path
verbose	logical indicating to be verbose or not
cleanup	logical to toggle removal of all intermediary files

Value

returns a ggseg3d-atlas ready object

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