diff --git a/docs/Config-File.md b/docs/Config-File.md index 2f309f6..be3e922 100644 --- a/docs/Config-File.md +++ b/docs/Config-File.md @@ -36,8 +36,8 @@ project: # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT! parameters: - # If enabled pools multiple experiments from same paper into one experiment; Default: True - pool_experiments: True + # If enabled pools multiple experiments from same paper into one experiment; + pool_experiments: False # TFCE is a method for multiple comparison correction (Frahm et al., 2022) tfce_enabled: True @@ -46,38 +46,46 @@ parameters: gm_masking: True # Size of bins used in MA histogram - bin_steps: 0.0001 # Default: 0.0001 + # Default: 0.0001 + bin_steps: 0.0001 # If enabled uses xgboost models to predict cutoffs instead of monte carlo simulation (Frahm et al., 2024) cutoff_predict_enabled: True # P-value required for significance # !! ONLY IF CUTOFF PREDICT IS DISABLED, OTHERWISE WON'T HAVE EFFECT !! - significance_threshold: 0.05 # Default: 0.05 + # Default: 0.05 + significance_threshold: 0.05 # Preliminary cluster forming threshold used in cluster-level family wise error correction # !! ONLY IF CUTOFF PREDICT IS DISABLED, OTHERWISE WON'T HAVE EFFECT !! - cluster_forming_threshold: 0.001 # Default: 0.001 + # Default: 0.001 + cluster_forming_threshold: 0.001 # Iterations used for monte-carlo based multiple comparison correction # !! ONLY IF CUTOFF PREDICT IS DISABLED, OTHERWISE WON'T HAVE EFFECT !! - monte_carlo_iterations: 5000 # Default: 5000 + # Default: 5000 + monte_carlo_iterations: 5000 # N subsamples calculated for probabilistic ALE algorithm - subsample_n: 2500 # Default: 2500 + # Default: 2500 + subsample_n: 2500 # Iterations used in classic contrast algorithm - contrast_permutations: 10000 # Default: 10000 + # Default: 10000 + contrast_permutations: 10000 # Correction Method on which to base contrast algorithm - contrast_correction_method: "cFWE" # Default: "cFWE"; Options: "cFWE", "vFWE", "tfce" + # Default: "cFWE"; Options: "cFWE", "vFWE", "tfce" + contrast_correction_method: "cFWE" # Sub-Iterations used in balanced contrast algorithm - difference_iterations: 1000 # Default: 1000 + # Default: 1000 + difference_iterations: 1000 # Number of parallel processes used for many different steps in the ALE algorith - maximum depends on your machine - nprocesses: 2 # Default: 2 - + # Default: 2 + nprocesses: 2 # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT @@ -85,14 +93,22 @@ parameters: # MA_Clustering Parameters # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT! clustering_parameters: - max_clusters: 10 # Default: 10 - subsample_fraction: 0.9 # Default: 0.9 - sampling_iterations: 1000 # Default: 1000 - null_iterations: 5000 # Default: 5000 - correlation_type: "spearman" # Default: "spearman"; Options: "spearman", "pearson" - clustering_method: "hierarchical" # Default: "hierarchical"; Options: "hierarchical", "kmeans" - linkage_method: "complete" # Default: "complete"; Options: "complete", "average", "ward" - use_pooled_std: False # Default: False +max_clusters: 10 # Default: 10 + +subsample_fraction: 0.9 # Default: 0.9 + +sampling_iterations: 1000 # Default: 1000 + +null_iterations: 5000 # Default: 5000 + +correlation_type: "spearman" # Default: "spearman"; Options: "spearman", "pearson" + +clustering_method: "hierarchical" # Default: "hierarchical"; Options: "hierarchical", "kmedoids" + +linkage_method: "complete" # Default: "complete"; Options: "complete", "average" + +use_pooled_std: False # Default: False + # DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT ```