search

pyplati / platipy

Processing Library and Analysis Toolkit for Medical Imaging in Python
https://pyplati.github.io/platipy/
Apache License 2.0
111 stars 27 forks source link

Issues running cardiac segmentation example in collab #281

Open haydon1999 opened 1 month ago

haydon1999 commented 1 month ago

I keep getting this error saying a post processing file is missing for the cardiac segmentation sample.

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 /home/haydon/.platipy/nnUNet_models/nnUNet/3d_lowres/Task400_OPEN_HEART_1FOLD/nnUNetTrainerV2__nnUNetPlansv2.1

I have tried running the example in collab as well as locally and am getting the same error. Any ideas how to fix this? Thanks so much.

pchlap commented 1 month ago

Hi @haydon1999, this warning message about postprocessing isn't critical and can be ignored (this is shown by nnUNet since we didn't train the DL model across multiple folds).

If the code is hanging at that point and you're not getting the results you expect, perhaps something else is going wrong, or the code is just taking some time to complete. Can you check that you have your Colab notebook is running as T4 GPU?

I just ran through the notebook on colab successfully. It does pause for a while right where that warning message shows. This is a bit unfortunate but I believe this is where atlas registration part comes in which takes some time to process. Also, connection to Zenodo can sometimes be slow and it might take a few minutes to download the atlas, but this only happens on the first run on your system (or Colab session). In total it took around 10 mins to run through the notebook from start to finish on Colab for me just now.

You can also check out some suggestions I made in here as someone else was having a similar issue: #275

Let me know how you go.