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Simulate a longitudinal brain surface dataset with associated phenotype data

Source: R/simulate_dataset.R
simulate_dataset.Rd

Generates a synthetic longitudinal dataset for multiple sites/cohorts, each with multiple timepoints/sessions per subject. The function produces:

  • Brain surface data in FreeSurfer .mgh format, organised in a verywise folder structure (see vignettes for details).

  • A matching pheno data frame with mock participant sex and age, saved as "phenotype.csv" in the path directory.

This is useful for testing pipelines or demonstrations where realistic FreeSurfer-style data and phenotypic information are required.

Usage

simulate_dataset(
  path,
  data_structure = list(cohort1 = list(sessions = c("01", "02", "03"), n_subjects = 10),
    cohort2 = list(sessions = c("01", "02"), n_subjects = 20)),
  fs_template = "fsaverage",
  simulate_association = NULL,
  overwrite = TRUE,
  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

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).

overwrite

Logical (default = TRUE). Whether to overwrite an existing phenotype file.

seed

Integer (default = 3108). Random seed.

verbose

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

...

Additional arguments passed to simulate_freesurfer_data.

Value

Invisibly returns NULL. Data and phenotype files are written to path.

See also

simulate_freesurfer_data, simulate_long_pheno_data

Author

Serena Defina, 2024.