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nnUNetv2_plan_and_preprocess stuck at preprocessing (99%) #2585

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johnson111788 opened this issue Nov 6, 2024 · 0 comments
Open

nnUNetv2_plan_and_preprocess stuck at preprocessing (99%) #2585

johnson111788 opened this issue Nov 6, 2024 · 0 comments
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@constantinulrich

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@johnson111788
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Hi,

Similar to #1494 (comment), my nnUNetv2_plan_and_preprocess stopped at 99% (5048/5097 3D CT scans with 0.5mm spacing).
image

My preprocess command is nnUNetv2_plan_and_preprocess -d 1014 -npfp 64 -np 64 -c 3d_fullres and I've already acquired these files:
image,
where 5048 pkl and 5048 npz files are generated in ./nnUNetPlans_3d_fullres.

I've checked the process
image
, the CPU
image
, and the storage
image.

It seems like the preprocessing just stopped. May I know if I can simply abandon the unfinished cases? If so, what should I do?
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@johnson111788 @constantinulrich