write.region.values: Write one value per atlas region for a subject.

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

Write one value per atlas region for a subject.

Description

Given an atlas and a list that contains one value for each atlas region, write a morphometry file in which all region vertices are assigned the value. Can be used to plot stuff like p-values or effect sizes onto brain regions.

Usage

write.region.values(
  subjects_dir,
  subject_id,
  hemi,
  atlas,
  region_value_list,
  outfile_morph_name,
  format = "mgz",
  do_write_file = TRUE,
  output_path = NULL,
  value_for_unlisted_regions = NaN
)

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
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.

Value

a named list with the following entries: "data": a vector containing the data. "file_written": string, path to the file that was written, only exists if do_write = TRUE.

See Also

Other output functions: write.region.aggregated(), write.region.values.fsaverage()

Examples

## Not run: 
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   region_value_list = list("bankssts"=0.9, "precuneus"=0.7);
   write.region.values(subjects_dir, 'subject1', 'lh', 'aparc',
    region_value_list, 'pvalues.mgz', do_write_file = FALSE);

## End(Not run)

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