group.morph.native: Retrieve native space morphometry data for a group of...

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

Retrieve native space morphometry data for a group of subjects.

Description

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

Usage

group.morph.native(
  subjects_dir,
  subjects_list,
  measure,
  hemi,
  format = "curv",
  cortex_only = 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.
subjects_list,	vector of strings. The subject identifiers.
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 subjects. Defaults to FALSE.

Value

named list with native space morph data, the names are the subject identifiers from the subjects_list, and the values are morphometry data vectors (of different length, as each subject has a different vertex count in native space).

See Also

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

Examples

## Not run: 
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   subjects_list = c("subject1", "subject2");
   data = group.morph.native(subjects_dir, subjects_list, "thickness", "lh");

## End(Not run)

dfsp-spirit/nitools documentation built on Jan. 26, 2024, 8:24 p.m.