write.region.aggregated: Write data aggregated over regions to morphometry file for...

Description Usage Arguments See Also

View source: R/morph_atlas_agg.R

Description

Given an atlas, a subjects list and a measure, aggregate the measure over each region (e.g., mean) and write an output morphometry file in which the value for all region vertices is set to the aggregated value.

Usage

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write.region.aggregated(
  subjects_dir,
  subjects_list,
  measure,
  hemi,
  atlas,
  agg_fun = mean,
  outfile_morph_name = "",
  format = "mgz"
)

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,

string vector. A vector of subject identifiers that match the directory names within subjects_dir.

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' 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.

agg_fun,

function. An R function that aggregates data, typically max, mean, min or something similar. Note: this is NOT a string, put the function name without quotes. Defaults to mean.

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'. Defaults to 'agg_<measure>'.

format,

string. A morphometry file format. One of 'mgh', 'mgz' or 'curv.' The output file name extension will be set accordingly. Defaults to 'mgz'.

See Also

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


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