[Python] cannot pickle 'module' object error in Anaconda prompt with nnUNetv2

I am trying to do preprocessing of nnUNetv2 on my desktop.

It did not work in Visual Studio, so I changed my environment to Anaconda prompt.

However, it has still the same issue with 'cannot pickle 'module' object'.

Anyone know how to fix this issue?

Thank you very much.


(nnunetv2) C:\Users\username\Research\nnUNet_raw>nnUNetv2_extract_fingerprint -d 1 --verbose
Dataset001_AirwaySegmentation
Using <module 'nibabel' from 'C:\\Users\\username\\AppData\\Local\\anaconda3\\envs\\nnunetv2\\lib\\site-packages\\nibabel\\__init__.py'> reader/writer
Traceback (most recent call last):
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\Scripts\nnUNetv2_extract_fingerprint.exe\__main__.py", line 7, in <module>
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_entrypoints.py", line 27, in extract_fingerprint_entry
extract_fingerprints(args.d, args.fpe, args.np, args.verify_dataset_integrity, args.clean, args.verbose)
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_api.py", line 46, in extract_fingerprints
extract_fingerprint_dataset(d, fingerprint_extractor_class, num_processes, check_dataset_integrity, clean,
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\site-packages\nnunetv2\experiment_planning\plan_and_preprocess_api.py", line 32, in extract_fingerprint_dataset
return fpe.run(overwrite_existing=clean)
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\site-packages\nnunetv2\experiment_planning\dataset_fingerprint\fingerprint_extractor.py", line 130, in run
results = ptqdm(DatasetFingerprintExtractor.analyze_case,
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\site-packages\acvl_utils\miscellaneous\ptqdm.py", line 34, in ptqdm
for i, result in p.imap_unordered(function_wrapper, enumerate(iterable), chunksize=chunksize):
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\multiprocessing\pool.py", line 868, in next
raise value
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\multiprocessing\pool.py", line 537, in _handle_tasks
put(task)
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\multiprocessing\connection.py", line 206, in send
self._send_bytes(_ForkingPickler.dumps(obj))
File "C:\Users\username\AppData\Local\anaconda3\envs\nnunetv2\lib\multiprocessing\reduction.py", line 51, in dumps
cls(buf, protocol).dump(obj)
TypeError: cannot pickle 'module' object


I installed Python==3.8 here, and all of required modules are configured,

for example, Pytorch, nibabel, SimpleITK, scikit-image, etc.

Also, I tried to use pathos, but it seems to only work in Python, not in Anaconda prompt.

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