Convert Label to Annotation

If you have labels rather than a full annotation file, these can be combined with FreeSurfer's mris_label2annot.

mris_label2annot(
  labels,
  ctab,
  hemisphere = "rh",
  subject = "fsaverage5",
  subjects_dir = fs_subj_dir(),
  annot_dir = file.path(subjects_dir, subject, "label"),
  output_dir = subjects_dir,
  opts = NULL,
  verbose = TRUE
)

Arguments

labels	label file path vector
ctab	colourtable file
hemisphere	hemisphere, either "rh" or "lh"
subject	Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
subjects_dir	Freesurfer subject directory
annot_dir	path to directory with annot-files
output_dir	output directory path
opts	other arguments to freesurfer command
verbose	logical indicating to be verbose or not

Examples

if(freesurfer::have_fs()){
# for freesurfer help see:
freesurfer::fs_help("mris_label2annot")

subj_dir <- freesurfer::fs_subj_dir()
# Split up aparc annot into labels
mri_annotation2label(annot_name = "aparc")

# get annot for colour labels
annot <- freesurfer::read_annotation(
              file.path(subj_dir, 
                        "fsaverage5/label/rh.aparc.annot"))

labels <- list.files(
   file.path(subj_dir, "fsaverage5/label/aparc"), 
    full.names = TRUE)

# Combine them again into annot.
mris_label2annot(labels, annot$colortable)

}