Swin UNETR Brats 0.2.1 #1593
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Hi @EdenSehatAI, could you please check your data? It looks like the data isn't in this location.
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data_dir = '/content/drive/MyDrive/EdenSehat/BraTS2021_Training_Data/TrainingData' Also for reference, |
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Then perhaps a permission issue, you could try to set the permission to everyone and try again. |
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Sorry where can I set the permission? |
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Doesn't work this time around I'm getting a different file that is error and not the previous one...I don't think it is a file_path error given that it has already run all the files 9 epochs prior. It always seem to get stuck on 9th epoch: RuntimeError Traceback (most recent call last) 5 frames RuntimeError: Caught RuntimeError in DataLoader worker process 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): The above exception was the direct cause of the following exception: Traceback (most recent call last): The above exception was the direct cause of the following exception: Traceback (most recent call last): |
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Hi,
In the notebook: https://github.com/Project-MONAI/tutorials/blob/main/3d_segmentation/swin_unetr_brats21_segmentation_3d.ipynb
I'm up to the training phase but am always getting this error on the 9th epoch. Why is this the case?
Val 9/50 221/250 , dice_tc: 0.7409106 , dice_wt: 0.837617 , dice_et: 0.78997755 , time 4.82s
Val 9/50 222/250 , dice_tc: 0.74006385 , dice_wt: 0.8375687 , dice_et: 0.7895737 , time 4.82s
RuntimeError Traceback (most recent call last)
in <cell line: 11>()
9 loss_epochs,
10 trains_epoch,
---> 11 ) = trainer(
12 model=model,
13 train_loader=train_loader,
5 frames
/usr/local/lib/python3.10/dist-packages/torch/_utils.py in reraise(self)
692 # instantiate since we don't know how to
693 raise RuntimeError(msg) from None
--> 694 raise exception
695
696
RuntimeError: Caught RuntimeError in DataLoader worker process 1.
Original Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/nibabel/loadsave.py", line 90, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/content/drive/MyDrive/EdenSehat/BraTS2021_Training_Data/TrainingData/TrainingData/BraTS2021_00390/BraTS2021_00390_flair.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/transform.py", line 141, in apply_transform
return _apply_transform(transform, data, unpack_items, lazy, overrides, log_stats)
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/transform.py", line 98, in _apply_transform
return transform(data, lazy=lazy) if isinstance(transform, LazyTrait) else transform(data)
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/io/dictionary.py", line 162, in call
data = self.loader(d[key], reader)
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/io/array.py", line 255, in call
img = reader.read(filename)
File "/usr/local/lib/python3.10/dist-packages/monai/data/image_reader.py", line 908, in read
img = nib.load(name, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/nibabel/loadsave.py", line 92, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/content/drive/MyDrive/EdenSehat/BraTS2021_Training_Data/TrainingData/TrainingData/BraTS2021_00390/BraTS2021_00390_flair.nii.gz'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/transform.py", line 141, in apply_transform
return _apply_transform(transform, data, unpack_items, lazy, overrides, log_stats)
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/transform.py", line 98, in _apply_transform
return transform(data, lazy=lazy) if isinstance(transform, LazyTrait) else transform(data)
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/compose.py", line 335, in call
result = execute_compose(
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/compose.py", line 111, in execute_compose
data = apply_transform(
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/transform.py", line 171, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7c01153aa680>
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/torch/utils/data/_utils/worker.py", line 308, in _worker_loop
data = fetcher.fetch(index)
File "/usr/local/lib/python3.10/dist-packages/torch/utils/data/_utils/fetch.py", line 51, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/usr/local/lib/python3.10/dist-packages/torch/utils/data/_utils/fetch.py", line 51, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/usr/local/lib/python3.10/dist-packages/monai/data/dataset.py", line 112, in getitem
return self._transform(index)
File "/usr/local/lib/python3.10/dist-packages/monai/data/dataset.py", line 98, in _transform
return apply_transform(self.transform, data_i) if self.transform is not None else data_i
File "/usr/local/lib/python3.10/dist-packages/monai/transforms/transform.py", line 171, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x7c01153abee0>
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