Closed fyb99 closed 9 months ago
Dear Fabian Isensee, I have met two problems during the data preprocessing and training phases when using nnUNet framework.
Hi, I was facing the same issue for days and found out what was going wrong.
for my case, the data was 2D (1, x, y) and the preprocessing made the "cannot convert float infinity to integer" error.
I read the article again, and found out that 2D data preprocessing should be little different
in the below, you can see how to handle 2D (1, x, y) data with the preprocessing
once this is completed, you can use the dataset like any other nnU-Net dataset. Note that since this is a 2D
dataset there is no need to run preprocessing for 3D U-Nets. You should therefore run the
`nnUNet_plan_and_preprocess` command like this:
> nnUNet_plan_and_preprocess -t 120 -pl3d None
not sure if this is your case, but hope it helps even a little
@fyb99 do you still face issues when using nnU-Net with 2D data?
thanks @provbs !
Please read the following resources before posting issues:
Common questions: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/common_questions.md
Common Problems and their solutions: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/common_problems_and_solutions.md
Expected epoch times and tips on how to identify bottlenecks: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/expected_epoch_times.md