fsbrain (version 0.5.5)

subject.morph.native: Retrieve native space morphometry data for a single subject.

Description

Load native space morphometry data (like 'surf/lh.area') for a subject from disk. Uses knowledge about the FreeSurfer directory structure to load the correct file.

Usage

subject.morph.native(
  subjects_dir,
  subject_id,
  measure,
  hemi,
  format = "curv",
  cortex_only = FALSE,
  split_by_hemi = FALSE
)

Value

vector with native space morph data, as returned by read.fs.morph.

Arguments

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

measure

string. Name of the vertex-wise measure of morphometry data file. E.g., "area" or "thickness". Used to construct the name of the morphometry file to be loaded.

hemi

string, one of 'lh', 'rh' or 'both'. The hemisphere name. Used to construct the names of the annotation and morphometry data files to be loaded.

format

string. One of 'mgh', 'mgz', 'curv'. Defaults to 'curv'.

cortex_only

logical, whether to mask the medial wall, i.e., whether the morphometry data for all vertices which are *not* part of the cortex (as defined by the label file `label/?h.cortex.label`) should be replaced with NA values. In other words, setting this to TRUE will ignore the values of the medial wall between the two hemispheres. If set to true, the mentioned label file needs to exist for the subject. Defaults to FALSE.

split_by_hemi

logical, whether the returned data should be encapsulated in a named list, where the names are from 'lh' and 'rh', and the values are the respective data.

See Also

Other morphometry data functions: apply.label.to.morphdata(), apply.labeldata.to.morphdata(), group.morph.native(), group.morph.standard(), subject.morph.standard()

Examples

if (FALSE) {
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");

   # Load the full data:
   thickness_lh = subject.morph.native(subjects_dir, "subject1", "thickness", "lh");
   mean(thickness_lh);  # prints 2.437466

   # Load the data again, but this time exclude the medial wall:
   thickness_lh_cortex = subject.morph.native(subjects_dir, "subject1", "thickness",
    "lh", cortex_only=TRUE);
   mean(thickness_lh_cortex, na.rm=TRUE);     # prints 2.544132
   vis.data.on.subject(subjects_dir, "subject1", thickness_lh_cortex, NULL);
}