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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. verywise expects the input data to be always registered on the "fsaverage" template and the final analyses should also 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.