Not able to pre process the dataset 04 LiTS

[aaekay]

python -W ignore label_transfer.py train len 131 Traceback (most recent call last): File "label_transfer.py", line 290, in for index, batch in enumerate(train_loader): File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 530, in next data = self._next_data() File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1224, in _next_data return self._process_data(data) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/utils/data/dataloader.py", line 1250, in _process_data data.reraise() File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/_utils.py", line 457, in reraise raise exception RuntimeError: Caught RuntimeError in DataLoader worker process 0. Original Traceback (most recent call last): File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/transform.py", line 89, in apply_transform return _apply_transform(transform, data, unpack_items) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/transform.py", line 53, in _apply_transform return transform(parameters) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/io/dictionary.py", line 131, in call data = self._loader(d[key], reader) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/io/array.py", line 213, in call img = reader.read(filename) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/data/imagereader.py", line 421, in read img = nib.load(name, **kwargs) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/nibabel/loadsave.py", line 115, in load raise ImageFileError(msg) nibabel.filebasedimages.ImageFileError: File /home/amit_g/scr/datasets/clip/04_LiTS/label/liver_0.nii.gz is not a gzip file

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/transform.py", line 89, in apply_transform return _apply_transform(transform, data, unpack_items) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/transform.py", line 53, in _apply_transform return transform(parameters) File "/home/amitg/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/compose.py", line 173, in call input = apply_transform(transform, input, self.map_items, self.unpack_items, self.log_stats) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/transform.py", line 113, in apply_transform raise RuntimeError(f"applying transform {transform}") from e RuntimeError: applying transform <monai.transforms.io.dictionary.LoadImaged object at 0x7fdab8d054f0>

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/utils/data/_utils/worker.py", line 287, in _worker_loop data = fetcher.fetch(index) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 49, in data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/data/dataset.py", line 97, in getitem return self._transform(index) File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/data/dataset.py", line 83, in _transform return apply_transform(self.transform, data_i) if self.transform is not None else data_i File "/home/amit_g/scratch/env/clip/lib/python3.8/site-packages/monai/transforms/transform.py", line 113, in apply_transform raise RuntimeError(f"applying transform {transform}") from e RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x7fdab746bfd0>

[ljwztc]

File /home/amit_g/scr/datasets/clip/04_LiTS/label/liver_0.nii.gz is not a gzip file Please check you data file or check the nib version

[aaekay]

which nibabel version is required? not mentioned in the requirements

[ljwztc]

the nibabel is included in monai. you can install through pip install 'monai[all]'