How to integrate my model into the Totalsegmentator Run

wasserth / TotalSegmentator

Tool for robust segmentation of >100 important anatomical structures in CT and MR images

Apache License 2.0

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How to integrate my model into the Totalsegmentator Run #357

Closed tedi14 closed 2 months ago

tedi14 commented 2 months ago

Hello,

I have my own trained nnunet model and was able to run predictions on different data. I was wondering where in Totalsegmentator can I find the model itself of Totalsegmentator? Where is it's checkpoint.pth file, folds etc? In which folder is the model itself kept?

Thank you

wasserth commented 2 months ago

You need to make edits at several lines in several files if you want to use your own nnU-Net model. Thus, it is not straight forward. I recommend to simply run your nnU-Net independently of TotalSEgmentator.