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Simulate longitudinal FreeSurfer vertex-wise data

Source: R/simulate_dataset.R
simulate_freesurfer_data.Rd

Simulates FreeSurfer-formatted brain surface data for multiple cohorts/sites and multiple timepoints/sessions. The output folder structure emulates that produced by the FreeSurfer recon-all command, with directories named: sub-<ID>_ses-<SESSION>.

The vertex-wise data are stored as .mgh files, with optional simulation of an association with a phenotype variable.

Usage

simulate_freesurfer_data(
  path,
  data_structure = list(cohort1 = list(sessions = c("01", "02"), n_subjects = 100),
    cohort2 = list(sessions = c("01", "02"), n_subjects = 150)),
  fs_template = "fsaverage",
  measure = "thickness",
  hemi = "lh",
  fwhmc = "fwhm10",
  vw_mean = 6.5,
  vw_sd = 0.5,
  simulate_association = NULL,
  seed = 3108,
  verbose = TRUE
)

Arguments

path

Character string. Directory where the dataset should be created. Will be created if it does not exist.

data_structure

Named list defining cohorts/sites. Each element is a list with:

"sessions"

Character vector of session labels.

"n_subjects"

Integer number of subjects.

fs_template

Character (default = "fsaverage"). FreeSurfer template for vertex registration. This is used to determine the size of the synthetic brain surface data. Options:

  • "fsaverage" = 163842 vertices (highest resolution)

  • "fsaverage6" = 40962 vertices

  • "fsaverage5" = 10242 vertices

  • "fsaverage4" = 2562 vertices

  • "fsaverage3" = 642 vertices

measure

Character (default = "thickness"). Surface measure to simulate. This is used for file names.

hemi

Character (default = "lh"). Hemisphere code: "lh" (left) or "rh" (right). This is used for file names.

fwhmc

Character (default = "fwhm10"). Full-width half maximum smoothing parameter. This is used for file names.

vw_mean

Numeric (default = 6.5). Mean of the simulated vertex-wise values.

vw_sd

Numeric (default = 0.5). Standard deviation of the simulated vertex-wise values.

simulate_association

Optional. If numeric, must be of length equal to the number of generated files; if character, must have the format "<beta> * <variable_name>". Associations are injected into one small region (the entorhinal cortex).

seed

Integer (default = 3108). Random seed.

verbose

Logical (default = TRUE). If TRUE, print progress messages.

Value

Invisibly returns NULL. Vertex-wise data are written to path in FreeSurfer-compatible format.

See also

simulate_dataset, simulate_long_pheno_data

Author

Serena Defina, 2024.