Re-register an annotation file — mri_surf2surf

Annotation files are subject specific. Most are registered for fsaverage, but we recommend using fsaverage5 for the mesh plots in ggseg3d, as these contain a decent balance in number of vertices for detailed rendering and speed.

Usage

mri_surf2surf_rereg(
  subject,
  annot,
  hemisphere = c("lh", "rh"),
  target_subject = "fsaverage5",
  output_dir = as.character(fs::path(freesurfer::fs_subj_dir(), subject, "label")),
  verbose = get_verbose()
)

Arguments

subject: subject the original annotation file is registered to
annot: annotation file name (as found in subjects_dir)
hemisphere: hemisphere (one of "lh" or "rh")
target_subject: subject to re-register the annotation (default fsaverage5)
output_dir: Where to write the re-registered annotation. Defaults to subject's own label/ directory inside FreeSurfer's SUBJECTS_DIR, beside the annotation being re-registered - so the default writes into your FreeSurfer installation, not a temporary directory. Pass a path of your own to write elsewhere.
verbose: How much to print: 0 silent, 1 progress (the default), 2 adds FreeSurfer's own output. TRUE and FALSE mean 1 and 0. Falls back to options("ggseg.extra.verbose"), then GGSEG_EXTRA_VERBOSE.

Value

The command's exit status, invisibly. Called for the annotation file it writes to output_dir.

Examples

if (FALSE) { # \dontrun{
# For help see:
freesurfer::fs_help("mri_surf2surf")

mri_surf2surf_rereg(
  subject = "bert",
  annot = "aparc.DKTatlas",
  target_subject = "fsaverage5"
)
} # }