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I'm coming from V1 but this issue is for newcomers,
Is is possible to add a link to setting_up_paths.md inside the first pages of the documentation as it is required for running the whole pipeline ?
Furthermore, the output of the nnUNetv2_convert_old_nnUNet_dataset could be made more explicit if the user hasn't set the environment variables properly. Currently, the output is :
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. f this is not intended, please read documentation/setting_up_paths.md for information on how to set this up properly.
nnUNet_preprocessed is not defined and nnU-Net can not be used for preprocessing or training. If this is not intended, please read documentation/setting_up_paths.md for information on how to set this up.
nnUNet_results is not defined and nnU-Net cannot be used for training or inference. If this is not intended behavior, please read documentation/setting_up_paths.md for information on how to set this up.
Traceback (most recent call last):
File "/pasteur/appa/homes/rocremes/mambaforge/envs/monai-env/bin/nnUNetv2_convert_old_nnUNet_dataset", line 8, in <module>
sys.exit(convert_entry_point())
File "/pasteur/appa/homes/rocremes/mambaforge/envs/monai-env/lib/python3.9/site-packages/nnunetv2/dataset_conversion/convert_raw_dataset_from_old_nnunet_format.py", line 53, in convert_entry_point
convert(args.input_folder, args.output_dataset_name)
File "/pasteur/appa/homes/rocremes/mambaforge/envs/monai-env/lib/python3.9/site-packages/nnunetv2/dataset_conversion/convert_raw_dataset_from_old_nnunet_format.py", line 13, in convert
if isdir(join(nnUNet_raw, target_dataset_name)):
File "/pasteur/appa/homes/rocremes/mambaforge/envs/monai-env/lib/python3.9/posixpath.py", line 76, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
It could be reduced to the first lines in an error message.
The text was updated successfully, but these errors were encountered:
I'm coming from V1 but this issue is for newcomers,
Is is possible to add a link to setting_up_paths.md inside the first pages of the documentation as it is required for running the whole pipeline ?
I'm thinking either in :
Furthermore, the output of the
nnUNetv2_convert_old_nnUNet_dataset
could be made more explicit if the user hasn't set the environment variables properly. Currently, the output is :It could be reduced to the first lines in an error message.
The text was updated successfully, but these errors were encountered: