nnunet error

[YingdiZhang]

Thanks for the great job. I‘m trying the nnunetV2 in MONAI， when running the command：
python -m monai.apps.nnunet nnUNetV2Runner run --input_config='./input.yaml' it occurs an error：
Failed to load image Python extension: /home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/torchvision/image.so: undefined symbol: _ZN3c104cuda20CUDACachingAllocator12recordStreamERKNS_7DataPtrENS0_10CUDAStreamE
2023-10-04 12:09:54,317 - WARNING - Dataset with the same ID exists!
2023-10-04 12:09:54,379 - INFO - Fingerprint extraction...
Dataset001_Task908_60VertCancellus
Traceback (most recent call last):
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/monai/apps/nnunet/main.py", line 20, in
fire.Fire({"nnUNetV2Runner": nnUNetV2Runner})
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/fire/core.py", line 141, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/fire/core.py", line 475, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/fire/core.py", line 691, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/monai/apps/nnunet/nnunetv2_runner.py", line 954, in run
self.plan_and_process()
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/monai/apps/nnunet/nnunetv2_runner.py", line 481, in plan_and_process
self.extract_fingerprints(fpe, npfp, verify_dataset_integrity, clean, verbose)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/monai/apps/nnunet/nnunetv2_runner.py", line 325, in extract_fingerprints
extract_fingerprints([int(self.dataset_name_or_id)], fpe, npfp, verify_dataset_integrity, clean, verbose)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 47, in extract_fingerprints
extract_fingerprint_dataset(d, fingerprint_extractor_class, num_processes, check_dataset_integrity, clean,
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/nnunetv2/experiment_planning/plan_and_preprocess_api.py", line 32, in extract_fingerprint_dataset
fpe = fingerprint_extractor_class(dataset_id, num_processes, verbose=verbose)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/nnunetv2/experiment_planning/dataset_fingerprint/fingerprint_extractor.py", line 34, in init
self.dataset = get_filenames_of_train_images_and_targets(self.input_folder, self.dataset_json)
File "/home/zyd/anaconda3/envs/monai1.2nnunet/lib/python3.9/site-packages/nnunetv2/utilities/utils.py", line 61, in get_filenames_of_train_images_and_targets
identifiers = get_identifiers_from_splitted_dataset_folder(join(raw_dataset_folder, 'imagesTr'), dataset_json['file_ending'])
KeyError: 'file_ending'

[KumoLiu]

Hi @YingdiZhang, did you create the dataset referring to this link?
https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/dataset_format.md#how-to-use-decathlon-datasets
https://github.com/MIC-DKFZ/nnUNet/blob/de48541317a8019668cfb37a354da241040fe3ce/nnunetv2/dataset_conversion/convert_MSD_dataset.py#L109