Hausdorf Distance not in summary.json

[i-moes]

Hi, I want to compute the HD for my segmentation task. I noticed that this is computed in metrics.py. However, the HD, AHD, and HD95 are not returned in the summary.json files. Do I need change something in order to have this metric printed in there as well?
Thank you!

[FabianIsensee]

Use this function:

nnUNet/nnunet/evaluation/evaluator.py

Line 446 in 7f1e273

def evaluate_folder(folder_with_gts: str, folder_with_predictions: str, labels: tuple, **metric_kwargs):

with advanced=True

[i-moes]

Thank you Fabian. I did use nnUnet_evaluate_folder. But, without advanced=True. 

I do, however, run it on a GPU via sbatch/.sh, where -h does not state an input option for the advanced setting. Do you know whether one can still run it with this advanced setting in this way?

[FabianIsensee]

Write your own eval script with using the function I linked above

[i-moes]

That makes total sense! Got it, thank you Fabian.