WARNING! Cannot run postprocessing because the postprocessing file is missing.

[agatadefr]

Hi Guys,

I got a problem with warning like this : WARNING! Cannot run postprocessing because the postprocessing file is missing. Make sure to run consolidate_folds in the output folder of the model first! The folder you need to run this in is /results/nnUNet/3d_fullres/Task500/nnUNetTrainerV2__nnUNetPlansv2.1

Hmm... I am not sure what to do ? Should I run something after training ? I would appreciate any advice please.

Best, Agata

[FabianIsensee]

Use nnUNet_determine_postprocessing :-)

[KamalRajSinghIITR]

Once required models (two or more than two i.e. 2d and 3d_fullres) are trained, use the following command to automatically determine what U-Net configuration(s) to use for test set prediction: nnUNet_find_best_configuration -m 2d 3d_fullres -t XXX This will generate a postprocessing.json file in processed folder.

Then run nnUNet_ensemble -f FOLDER1 FOLDER2 ... -o OUTPUT_FOLDER -pp POSTPROCESSING_FILE

[jielingao]

Maybe, In the output files, you have a file name 'plans.pkl' before you running inference, so delete 'plans.pkl' first, then run inference

[LIKP0]

That really help! Thank you very much!

[LCPPPPPPP]

Maybe, In the output files, you have a file name 'plans.pkl' before you running inference, so delete 'plans.pkl' first, then run inference

How does it work?