68 lines
No EOL
2.5 KiB
YAML
68 lines
No EOL
2.5 KiB
YAML
# Project Folder
|
|
project:
|
|
analysis_info: "analysis_info.xlsx"
|
|
experiment_info: "experiment_info.xlsx"
|
|
|
|
|
|
# ALE Parameters
|
|
# DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT!
|
|
parameters:
|
|
|
|
# If enabled pools multiple experiments from same paper into one experiment; Default: False
|
|
pool_experiments: False
|
|
|
|
# TFCE is a method for multiple comparison correction (Frahm et al., 2022)
|
|
tfce_enabled: True
|
|
|
|
# if enabled ALE map (and therefore all following maps) will be masked by ICBM 10% GM mask
|
|
gm_masking: True
|
|
|
|
# Size of bins used in MA histogram
|
|
bin_steps: 0.0001 # Default: 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
|
|
|
|
# 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
|
|
|
|
# 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
|
|
|
|
# N subsamples calculated for probabilistic ALE algorithm
|
|
subsample_n: 2500 # Default: 2500
|
|
|
|
# Iterations used in classic contrast algorithm
|
|
contrast_permutations: 10000 # Default: 10000
|
|
|
|
# Correction Method on which to base contrast algorithm
|
|
contrast_correction_method: "cFWE" # Default: "cFWE"; Options: "cFWE", "vFWE", "tfce"
|
|
|
|
# Sub-Iterations used in balanced contrast algorithm
|
|
difference_iterations: 1000 # Default: 1000
|
|
|
|
# Number of parallel processes used for many different steps in the ALE algorith - maximum depends on your machine
|
|
nprocesses: 2 # Default: 2
|
|
|
|
|
|
|
|
# DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT
|
|
|
|
# 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", "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 |