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).
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 )
| 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 |
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") }