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

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

Retrieve standard space morphometry data for a group of subjects.

Description

Load standard 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.standard(
  subjects_dir,
  subjects_list,
  measure,
  hemi = "both",
  fwhm = "10",
  template_subject = "fsaverage",
  format = "mgh",
  cortex_only = FALSE,
  df = FALSE,
  df_t = 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.
fwhm	string. Smoothing as string, e.g. '10' or '25'.
template_subject	string. Template subject name, defaults to 'fsaverage'.
format	string. One of 'mgh', 'mgz', 'curv'. Defaults to 'mgh'.
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 template subject. Defaults to FALSE.
df	logical, whether to return a dataframe instead of the named list. The dataframe will have one subject per column, and *n* rows, where *n* is the number of vertices of the template subject surface.
df_t	logical, whether to return a transposed dataframe. Only one of df or df_t must be TRUE.

Value

named list with standard space morph data, the names are the subject identifiers from the subjects_list, and the values are morphometry data vectors (all with identical length, the data is mapped to a template subject).

See Also

Other morphometry data functions: apply.label.to.morphdata(), apply.labeldata.to.morphdata(), group.morph.native(), 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");
   fulldata = group.morph.standard(subjects_dir, subjects_list, "thickness", "lh", fwhm='10');
   mean(fulldata$subject1);

   cortexdata = group.morph.standard(subjects_dir, subjects_list, "thickness",
    "lh", fwhm='10', cortex_only=FALSE);
   mean(cortexdata$subject1, na.rm=TRUE);

## End(Not run)

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