I keep getting an error; nnU-Net cannot see myraw dataset. Even though i've tried setting environment variables and renaming folders, when i try to run nnUNetv2_plan_and_preprocess it reports: nnUNet_raw=None. $Env:nnUNet_raw_data_base is set in PowerShell, but nnU-Net (Python) is not picking it up. I have tried and tried for hours but I just can't figure out what's causing the issue. Does anyone have any idea of what I could try? Thank you in advance!
Created by Abel Koffeman JustBeSimple I think your environment variable names are incorrect.
You can refer https://github.com/LISAChallengeOfficial/2024Task2/blob/master/documentation/set_environment_variables.md
export nnUNet_raw="/media/fabian/nnUNet_raw"
export nnUNet_preprocessed="/media/fabian/nnUNet_preprocessed"
export nnUNet_results="/media/fabian/nnUNet_results" I ran
PS C:\Users\Gebruiker\Documents\CodingProjects\2024task2> $env:nnUNet_raw_data_base="C:\Users\Gebruiker\Documents\CodingProjects\2024Task2\nnUNet_raw"
PS C:\Users\Gebruiker\Documents\CodingProjects\2024task2> $env:nnUNet_preprocessed="C:\Users\Gebruiker\Documents\CodingProjects\2024Task2\nnUNet_preprocessed"
PS C:\Users\Gebruiker\Documents\CodingProjects\2024task2> $env:RESULTS_FOLDER="C:\Users\Gebruiker\Documents\CodingProjects\2024Task2\nnUNet_trained_models"
PS C:\Users\Gebruiker\Documents\CodingProjects\2024task2> C:\Users\Gebruiker\anaconda3\Scripts\nnUNetv2_plan_and_preprocess.exe -t 999 --verify_dataset_integrity
nnUNet_raw is not defined and nnU-Net can only be used on data for which preprocessed files are already present on your system. nnU-Net cannot be used for experiment planning and preprocessing like this. If this is not intended, please read documentation/setting_up_paths.md for information on how to set this up properly.
i have my data like this: C:\Users\Gebruiker\Documents\CodingProjects\2024Task2\nnUNet_raw\Dataset999_LISA\imagesTr\lisa_0001_0000.nii.gz
C:\Users\Gebruiker\Documents\CodingProjects\2024Task2\nnUNet_raw\Dataset999_LISA\labelsTr\lisa_0001.nii.gz