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MIC-DKFZ / Skeleton-Recall

Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures
Apache License 2.0
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Adding Skeleton-Recall to Existing nnUNetv2 installation #2

Open rohand24 opened 1 month ago

rohand24 commented 1 month ago

Hi,

Is it possible to add Skeleton-recall trainer to existing nnUNetv2 installation?

I am able to figure out the skelton-recall trainer in the variants directory of trainers. If i copy that to my nnUNetv2 installation, will it work out of the box?

Regards, Rohan Dhamdhere

mrokuss commented 1 month ago

Hi @rohand24,

Thank you for reaching out.

The Skeleton-Recall Trainer is not yet included in the official nnUNetv2 release, but we are currently discussing ways to integrate it in the future.

For now, if you'd like to incorporate it into your existing nnUNetv2 installation, you would need to do more than just copy the nnUNetTrainerSkeletonRecall class. You'd also have to integrate the skeletonization process during data loading, which you can find here, as well as the custom loss function here and the compound loss combination here.

Let me know if you need further assistance!

Best, Max