nnunet_run_plan_and_preprocessing script

Run nnUNet command to extract dataset fingerprints, create experiment plan, preprocessing and ( optionally ) verify the dataset integrity. The CL script called is nnUNetv2_plan_and_preprocess, with the arguments extracted from the given configuration file.

usage: nnunet_run_plan_and_preprocessing [-h] --config-file CONFIG_FILE
                                         [--n-workers N_WORKERS] [-v | -q]

Named Arguments

--config-file

File path for the configuration dictionary, used to retrieve experiments variables (Task_ID)

--n-workers

Number of parallel processes used when pre-processing and unpacking the image data (Default: N_THREADS)

-v, --verbose

Enable verbose output in terminal. Add multiple times to increase verbosity.

-q, --silent

Suppress most log outputs in terminal.

Example call:

nnunet_run_plan_and_preprocessing.py --config-file /PATH/TO/CONFIG_FILE.json