Skip to contents

Build "supersubject" by stacking all vertex data in one large file-backed matrix with dimensions n_subjects x n_vertices.

Source: R/build_supersubject.R
build_supersubject.Rd

Build "supersubject" by stacking all vertex data in one large file-backed matrix with dimensions n_subjects x n_vertices.

Usage

build_supersubject(
  subj_dir,
  folder_ids,
  supsubj_dir,
  measure,
  hemi,
  n_cores,
  fwhmc = "fwhm10",
  fs_template = "fsaverage",
  backing,
  error_cutoff = 20,
  save_rds = FALSE,
  verbose = TRUE
)

Arguments

subj_dir

: path to the FreeSurfer data, this expects a verywise structure.

folder_ids

: the vector of observations to include. This holds the relative path (from subj_dir) to the FreeSurfer data folder (e.g. "site1/sub-1_ses-01").

supsubj_dir

: output path, where logs, backing files and the matrix itself (if save_rds == TRUE) will be stored.

measure

: vertex-wise measure, used to identify files.

hemi

: hemisphere, used to identify files.

n_cores

: number of cores to use for parallel processing.

fwhmc

: (default = "fwhm10") full-width half maximum value, used to identify files.

fs_template

: (default = "fsaverage") template on which to register vertex-wise data. The following values are accepted:

  • fsaverage (default) = 163842 vertices (highest resolution),

  • fsaverage6 = 40962 vertices,

  • fsaverage5 = 10242 vertices,

  • fsaverage4 = 2562 vertices,

  • fsaverage3 = 642 vertices Note that, at the moment, these are only used to downsample the brain map, for faster model tuning. The final analyses should be run using fs_template = "fsaverage" to avoid (small) imprecisions in vertex registration and smoothing.

backing

: (default = supsubj_dir) location to save the matrix backingfile.

error_cutoff

: (default = 20) how many missing directories or brain surface files for the function to stop with an error. If < error_cutoff directories/files are not found a warning is thrown and missing files are registered in the issues.log file.

save_rds

: (default = FALSE) save the supersubject file metadata for re-use in other sessions.

verbose

: (default = TRUE)

Value

A Filebacked Big Matrix with vertex data for all subjects (dimensions: n_subjects x n_vertices)

Author

Serena Defina, 2024.