blank_main_config.ini

[Default]
task=  # Type of standardized reporting: neuro_diagnosis, mediastinum_diagnosis
trace=  # true, false
caller=  # raidionics, slicer

[System]
ants_root= #Path to the install folder of a local cpp ANTs
gpu_id= #
output_folder= # Destination folder where the results will be saved
input_folder= # Folder path to the patient folder containing various radiological volumes
model_folder= # Folder path containing the model to use
pipeline_filename= # Filepath for the pipeline to execute

[Runtime]
non_overlapping=
reconstruction_method=  # thresholding, probabilities
reconstruction_order=  # resample_first, resample_second
use_stripped_data=  # True, False
use_registered_data=  # True, False

[Neuro]
brain_segmentation_filename= # Filepath pointing to an existing brain mask for the input patient
tumor_segmentation_filename= # Filepath pointing to an existing tumor mask for the input patient
cortical_features= #Atlas to include from: [MNI, Schaefer7, Schaefer17, Harvard-Oxford]
subcortical_features= # Atlas to include from: [BCB, BrainGrid]
braingrid_features = # Atlas to include from: [Voxels]

[Mediastinum]
lungs_segmentation_filename= # Filepath pointing to an existing lungs mask for the input patient
lobe_location= #NIY