nnunet_create_pipeline script

Run nnUNet pipeline:

Data and Folder Preparation -> Preprocessing -> Training.

usage: nnunet_create_pipeline [-h] -i INPUT_DATA_FOLDER --task-ID TASK_ID
                              [--test-split [0-100]] --config-file CONFIG_FILE
                              [--output-file OUTPUT_FILE]
                              [--extra-training-config EXTRA_TRAINING_CONFIG]
                              [-v | -q]

Named Arguments

-i, --input-data-folder

Input Dataset folder

--task-ID

Task ID used in the folder path tree creation.

--test-split

Possible choices: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100

Split value ( in % ) to create Test set from Dataset (Default: 20)

Default: 20

--config-file

Configuration JSON file with experiment and dataset parameters.

--output-file

Output TXT file path where to save the pipeline steps.

--extra-training-config

Optional JSON file path with nnUNet training configuration.

-v, --verbose

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

-q, --silent

Suppress most log outputs in terminal.

Example call:

nnunet_create_pipeline -i /path/to/input_data_folder --config-file nnUNet_3D_config.json --task-ID 000
nnunet_create_pipeline -i /path/to/input_data_folder --config-file nnUNet_3D_config.json --task-ID 000 --test-split 25