README.md

Simulations of alternative-based thresholding for the definition of fROIs

sims_multiple.R

In this file, the subject maps are simulated.

sims_multiple.sh

This file is used to submit to the linux-based supercomputer in order to simulate the brain maps.

sims_results.R

These files are used to analyze the simulated brain maps with both ABT and NHST. Voxels in different layers are counted.

sims_make_conditions.R

This file makes a table with all parameter configurations needed in sims_results. The resulting table is conditions_results.txt

sims_conditions_results….txt

These files represent the arrays needed for the loops in sims_results_multiple_….R and sims_results_anova.R respectively.

sims_rmask.txt

The mask with which the brain maps are simulated

sims_function.GLM.R

This file contains the function to estimate the parameters of the GLM, their standard error and the tmap

sims_results_multiple_….R

In these files, the information within each layer of the LSPM after ABT is evaluated. this is done for the different number of scans separately.

sims_results_anova.R

In this file anovas were performed in order to compute effect sizes for the simulation parameters contributing to the simulation design.

Real data example and evaluation of alternative-based thresholding for the definition of fROIs

Data

A toy data set in order to perform the cross-validation performed in the original study, as well as an overall brain mask for this “simulated individual”.

design.

These files contain information concerning the design of the fixed effects analysis in FSL, needed for the flameo command in real_es_groundtruth.sh

real_abt.R

In this file, NHST and ABT is performed on the left out run under different parameter configurations.

real_designCrossVal.R

Here, the design files mentioned above are made.

real_es_accuracy.R

In this file, the left out run is compared with the functionally relevant ground truth.

real_es_groundtruth.sh

Here, the ground truth of effect sizes for each step of the cross-validation is constructed.

real_writefiles.R

In this file, the overall brain mask for the “simulated individual” is constructed.