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

Description Usage Arguments Value See Also

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.fsaverage(
  hemi,
  atlas,
  region_value_list,
  output_file,
  template_subject = "fsaverage",
  template_subjects_dir = NULL,
  show_freeview_tip = FALSE,
  value_for_unlisted_regions = NaN
)

Arguments

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.

output_file,

string or 'NULL'. Path of the output file, including file name and extension. The format is determined from the (absence of a) file extension. If NULL, no file will be written.

template_subject

string, template subject name. Defaults to 'fsaverage'.

template_subjects_dir

string, the path to the subjects directory containing the template subject directory. If this is 'NULL', the function will try to find it using the environment, see the function find.subjectsdir.of for details. Defaults to NULL.

show_freeview_tip

logical, whether to print the freeview command on howto use the overlay to the console. (Only happens if the output_file is not 'NULL'.)

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()


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