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.
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_datasetcould 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.