blank_main_config.ini

[Default]
task=  # Task to perform, to sample from [heatmap, metrics]
input_folder=  # Folder containing the input cohort, with one subfolder per patient
output_folder=  # Existing destination folder where the results should be saved
ants_root=  # Path containing a local path containing a C++ version of ANTs (must have been built beforehand). By default, a Python version is used.

[Maps]
extra_parameters_filename=  # Path to a csv file containing additional information for each patient (e.g., image spacing)
use_registered_data=  # Boolean to indicate whether all inputs are already co-registered
gt_files_suffix=  # String with the class suffix, including file extension type (e.g., label_tumor.nii.gz)
registration_space=  # String to indicate which atlas to use for generate the maps, to sample from [MNI]
distribution_dense_parameters=  # For selecting a subset of the cohort, using a dense parameter featured in the extra_parameters_filename file, as a comma-separated string. The first value is the parameter name, and the second is a hyphen-separated list of thresholds (e.g., Age, 30-50-70)
distribution_categorical_parameters=  # For selecting a subset of the cohort, using a categorical parameter featured in the extra_parameters_filename file, as a comma-separated string. The first value is the parameter name, and the second is a subset of categories (e.g., Gender, F)
sequence_type=  # For specifying the MRI sequence, to sample from [T1w, T1-CE, T2, FLAIR]

[Metrics]
tumor_size=  # Boolean to decide whether to include size metrics or not. To sample from [True, False]
multifocality=  # Boolean to decide whether to include multifocality metrics or not. To sample from [True, False]
brain_location=  # Boolean to decide whether to include brain location metrics or not. To sample from [True, False]
cortical_features_location=  # List of strings to decide which cortical structures profile to use. To sample from [MNI, Schaefer7, Schaefer17, Harvard-Oxford]
subcortical_features_location=  # List of strings to decide which subcortical structures profile to use. To sample from [BCB]