Optional: simulating data

Serena Defina

2025-03-22

Data poor? Simulate yourself some data, son

If you are eager to get started with verywise but do not have access to a dataset (yet), you can generate both a set of ready-made FreeSurfer surface data files and a phenotype file to go with it.

The simulated dataset will already be saved into a verywise structure.

library(verywise)
#> Welcome, verywise user!
#> This is version: 0.1.3
#> For questions, issues, and bug reports, please see https://github.com/SereDef/verywise

Only generate the brain data

If you have a phenotype dataset already, but you are missing some FreeSurfer data, you can call the following function:

# Simulate FreeSurfer dataset
my_dataset_structure = list("cohort1" = list("sessions" = c("01", "02"),
                                             "n_subjects" = 100),
                            "cohort2" = list("sessions" = c("01", "02"),
                                             "n_subjects" = 150)
                            )
my_random_seed = 1984

simulate_freesurfer_data(path = "./VeryWiseUser/SimulatedExample",
                         data_structure = my_dataset_structure,
                         vw_resolution = 163842,
                         measure = "thickness",
                         hemi = "lh",
                         fwhmc = "fwhm10",
                         target = "fsaverage",
                         vw_mean = 6.5,
                         vw_sd = 0.5,
                         simulate_association = NULL,
                         seed = my_random_seed)

In this example, we are going to generate 500 left hemisphere ("lh") thickness maps. These maps belong to 250 fictional subjects, who all underwent 2 MRI sessions ("01" and "02") and belong to two cohorts ("cohort1" and "cohort2"). The resolution of these fake surface maps is 163842 vertices (corresponding to the most detailed FreeSurfer template "fsaverage"), and they will have an overall mean of 6.5 (mm thickness) and a standard deviation of 0.5.

You can also use the function to specify a simulated association with a variable of your choice. TODO

Only generate the phenotype data

On the other hand, if you already have some surfaces but you would like a phenotype to go with it you can use:

# Simulate phenotype dataset
simulate_long_pheno_data(data_structure = my_dataset_structure,
                         seed = my_random_seed)

This will generate a minimum “long format” dataframe with the variables you need, as well as simulated “sex” and “age” of the sample.

Alright, all in one go now

# Simulate FreeSurfer and phenotype dataset
simulate_data(path = "./VeryWiseUser/SimulatedExample", 
              data_structure = my_dataset_structure,
              simulate_association =  0.05 * pheno$age,
              overwrite = TRUE,
              seed = my_random_seed)

This will call simulate_long_pheno_data() and simulate_freesurfer_data() to give you everything you need to play around with verywise model fitting.