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

In dfsp-spirit/fsbrain: Managing and Visualizing Brain Surface Data

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
)

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.

Value

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

See Also

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

Examples

## Not run: 
   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);

## End(Not run)

dfsp-spirit/fsbrain documentation built on Nov. 28, 2024, 10:29 a.m.