- subjects_dir,
string. The FreeSurfer SUBJECTS_DIR, i.e., a directory containing the data for all your subjects, each in a subdir named after the subject identifier.
- subject_id,
string. The subject identifier
- hemi,
string, one of 'lh' or 'rh'. The hemisphere name. Used to construct the names of the annotation and morphometry data files to be loaded.
- atlas,
string. The atlas name. E.g., "aparc", "aparc.2009s", or "aparc.DKTatlas". Used to construct the name of the annotation file to be loaded.
- region_value_list,
named list. A list in which the names are atlas regions, and the values are the value to write to all vertices of that region.
- outfile_morph_name,
string. The measure part of the output file name. E.g., 'agg_thickness' will write the file '<subject>/surf/<hemi>.agg_thickness.mgh'.
- format,
string. A morphometry file format. One of 'mgh', 'mgz' or 'curv.' The output file name extension will be set accordingly. Defaults to 'mgz'.
- do_write_file,
logical. Whether to write the data to a file on the disk. If FALSE, the data are only returned (and the outfile_morph_name parameter gets ignored). Default to TRUE.
- output_path
string, path to the output directory. If omitted, defaults to the 'surf' directory of the subject (i.e., '<subjects_dir>/<subject_id>/surf/').
- value_for_unlisted_regions,
numeric scalar. The value to assign to vertices which are part of atlas regions that are not listed in region_value_list. Defaults to NaN.