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

Description Usage Arguments Value See Also Examples

View source: R/morph_atlas_agg.R

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

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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

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   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);

fsbrain documentation built on Sept. 16, 2021, 5:07 p.m.