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FAQ

Can I use a dictionary input instead of a "input.yaml" file?

Yes, nnUNetV2runner is relying on Google Fire Python library, which supports dictionary based input. The following is a concrete example.

## [pipeline] one-click solution with dict input
MODALITY="CT"
DATALIST="./msd_task09_spleen_folds.json"
DATAROOT="/workspace/data/Task09_Spleen"

python -m monai.apps.nnunet nnUNetRunner run --input "{'modality': '${MODALITY}', 'datalist': '${DATALIST}', 'dataroot': '${DATAROOT}'}"

I want to know more command examples

Sure! Please check out this documentation.

How to define multi-modal image inputs in the config file?

The modality key in the input yaml file accepts a list of strings as input. This example is prepared for the multi-modal MSD prostate dataset.