mris_label2annot: Convert Label to Annotation

In LCBC-UiO/ggsegExtra: Extra Utilities for the 'ggseg' and 'ggseg3d' Plotting Tools

Convert Label to Annotation

Description

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

Usage

mris_label2annot(
  labels,
  hemisphere = "rh",
  ctab,
  subject = "fsaverage5",
  subjects_dir = fs_subj_dir(),
  output_dir = subjects_dir,
  opts = NULL,
  verbose = TRUE
)

Arguments

labels	label file path vector
hemisphere	hemisphere, either "rh" or "lh"
ctab	colourtable file
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
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)

}

LCBC-UiO/ggsegExtra documentation built on May 9, 2022, 1:07 a.m.