I followed the instructions of the official pytorch implementation, but I got error when executing
"for FOLD in 0 1 2 3 4
do
nnUNet_train 3d_fullres nnUNetPlusPlusTrainerV2 Task003_Liver $FOLD
done"
The error is as fllows:PermissionError:
"Traceback (most recent call last):
File "/home/yang/python/anaconda/anaconda3/bin/nnUNet_train", line 33, in
sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_train')())
File "/home/yang/python/anaconda/anaconda3/bin/nnUNet_train", line 25, in importlib_load_entry_point
return next(matches).load()
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/importlib/metadata.py", line 86, in load
module = import_module(match.group('module'))
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/home/yang/UNetPlusPlus/pytorch/nnunet/run/run_training.py", line 18, in
from nnunet.run.default_configuration import get_default_configuration
File "/home/yang/UNetPlusPlus/pytorch/nnunet/run/default_configuration.py", line 17, in
from nnunet.paths import network_training_output_dir, preprocessing_output_dir, default_plans_identifier
File "/home/yang/UNetPlusPlus/pytorch/nnunet/paths.py", line 35, in
maybe_mkdir_p(nnUNet_raw_data)
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/site-packages/batchgenerators/utilities/file_and_folder_operations.py", line 53, in maybe_mkdir_p
os.makedirs(directory, exist_ok=True)
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/os.py", line 215, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/os.py", line 225, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/media/yang/nnUNet_raw_data_base' "
I use virtual machine of ubuntu system and want to run official code of official data.
I don't know if I should create the three files /nnUNet_raw_data_base/nnUNet_preprocessed/nnUNet_trained_models and put the data in it. Because I don't find where is the training data.
Thanks
I followed the instructions of the official pytorch implementation, but I got error when executing
"for FOLD in 0 1 2 3 4 do nnUNet_train 3d_fullres nnUNetPlusPlusTrainerV2 Task003_Liver $FOLD done"
The error is as fllows:PermissionError:
"Traceback (most recent call last): File "/home/yang/python/anaconda/anaconda3/bin/nnUNet_train", line 33, in
sys.exit(load_entry_point('nnunet', 'console_scripts', 'nnUNet_train')())
File "/home/yang/python/anaconda/anaconda3/bin/nnUNet_train", line 25, in importlib_load_entry_point
return next(matches).load()
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/importlib/metadata.py", line 86, in load
module = import_module(match.group('module'))
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/home/yang/UNetPlusPlus/pytorch/nnunet/run/run_training.py", line 18, in
from nnunet.run.default_configuration import get_default_configuration
File "/home/yang/UNetPlusPlus/pytorch/nnunet/run/default_configuration.py", line 17, in
from nnunet.paths import network_training_output_dir, preprocessing_output_dir, default_plans_identifier
File "/home/yang/UNetPlusPlus/pytorch/nnunet/paths.py", line 35, in
maybe_mkdir_p(nnUNet_raw_data)
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/site-packages/batchgenerators/utilities/file_and_folder_operations.py", line 53, in maybe_mkdir_p
os.makedirs(directory, exist_ok=True)
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/os.py", line 215, in makedirs
makedirs(head, exist_ok=exist_ok)
File "/home/yang/python/anaconda/anaconda3/lib/python3.9/os.py", line 225, in makedirs
mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/media/yang/nnUNet_raw_data_base' "
I use virtual machine of ubuntu system and want to run official code of official data. I don't know if I should create the three files /nnUNet_raw_data_base/nnUNet_preprocessed/nnUNet_trained_models and put the data in it. Because I don't find where is the training data. Thanks