mris_ca_label: MRI ca label

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

MRI ca label

Description

For a single subject, produces an annotation file, in which each cortical surface vertex is assigned a neuroanatomical label. This automatic procedure employs data from a previously-prepared atlas file. An atlas file is created from a training set, capturing region data manually drawn by neuroanatomists combined with statistics on variability correlated to geometric information derived from the cortical model (sulcus and curvature). Besides the atlases provided with FreeSurfer, new ones can be prepared using mris_ca_train).

Usage

mris_ca_label(
  subject = "fsaverage5",
  hemisphere = "lh",
  canonsurf = "sphere.reg",
  classifier = file.path(fs_dir(), "average/lh.DKTatlas40.gcs"),
  output_file,
  subjects_dir = fs_subj_dir(),
  opts = NULL
)

Arguments

subject	Freesurfer subject, must exist in whatever subject directory specified or set in the environment with $SUBJECTS_DIR
hemisphere	hemisphere, either "rh" or "lh"
canonsurf	canonical surface file. Ie: the name of the spherical surface file which describes the registration of a subject's vertices to the reference "average" surface. Example: sphere.reg
classifier	specify classifier array input file (atlas file)
output_file	path to output file
subjects_dir	Freesurfer subject directory
opts	other arguments to freesurfer command

Examples

if(freesurfer::have_fs()){
# for freesurfer help see:
freesurfer::fs_help("mris_ca_label")
mris_ca_label(output_file = "test.lh.annot")

mris_ca_label(hemisphere = "rh", output_file = "test.rh.annot")
}

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