Open dal50musc opened 7 months ago
I am trying to run an example of bidsmreye
I received this permission error when using the generalize action on bidsMReye. Error says it cannot write data to cache folder.
(base) Daniels-iMac:delete daniellench$ sudo docker run --rm -it \ --user "$(id -u):$(id -g)" \ -v $PWD/tests/data/moae_fmriprep:/home/neuro/data \ -v $PWD/outputs/moae_fmriprep/derivatives:/home/neuro/outputs/ \ cpplab/bidsmreye:latest \ /home/neuro/data/ /home/neuro/outputs/ participant \ --action generalize Password: whoami: cannot find name for user ID 501 2023-12-14 16:59:58.877876: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2023-12-14 16:59:59.109886: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory 2023-12-14 16:59:59.109944: I tensorflow/compiler/xla/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. 2023-12-14 16:59:59.903277: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory 2023-12-14 16:59:59.903473: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory 2023-12-14 16:59:59.903533: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly. [17:00:02] WARNING bidsMReye - [17:00:02] - Matplotlib created a temporary config/cache directory at /tmp/matplotlib-u0nw0afc because the default __init__.py:500 path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING [17:00:03] WARNING bidsMReye - [17:00:03] - log level: WARNING bidsmreye.py:112 ╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/pooch/utils.py:252 in │ │ make_local_storage │ │ │ │ 249 │ │ │ os.makedirs(path, exist_ok=True) │ │ 250 │ │ else: │ │ 251 │ │ │ action = "write to" │ │ ❱ 252 │ │ │ with tempfile.NamedTemporaryFile(dir=path): │ │ 253 │ │ │ │ pass │ │ 254 │ except PermissionError as error: │ │ 255 │ │ message = [ │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ action = 'write to' │ │ │ │ env = None │ │ │ │ message = [ │ │ │ │ │ "[Errno 13] Permission denied: '/home/neuro/bidsMReye/models/tmpe3lsq2cm'", │ │ │ │ │ "| Pooch could not write to data cache folder │ │ │ │ '/home/neuro/bidsMReye/models'.", │ │ │ │ │ 'Will not be able to download data files.' │ │ │ │ ] │ │ │ │ path = '/home/neuro/bidsMReye/models' │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/tempfile.py:545 in NamedTemporaryFile │ │ │ │ 542 │ if _os.name == 'nt' and delete: │ │ 543 │ │ flags |= _os.O_TEMPORARY │ │ 544 │ │ │ ❱ 545 │ (fd, name) = _mkstemp_inner(dir, prefix, suffix, flags, output_type) │ │ 546 │ try: │ │ 547 │ │ file = _io.open(fd, mode, buffering=buffering, │ │ 548 │ │ │ │ │ │ newline=newline, encoding=encoding, errors=errors) │ │ │ │ ╭─────────────────── locals ───────────────────╮ │ │ │ buffering = -1 │ │ │ │ delete = True │ │ │ │ dir = '/home/neuro/bidsMReye/models' │ │ │ │ encoding = None │ │ │ │ errors = None │ │ │ │ flags = 131266 │ │ │ │ mode = 'w+b' │ │ │ │ newline = None │ │ │ │ output_type = <class 'str'> │ │ │ │ prefix = 'tmp' │ │ │ │ suffix = '' │ │ │ ╰──────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/tempfile.py:255 in _mkstemp_inner │ │ │ │ 252 │ │ file = _os.path.join(dir, pre + name + suf) │ │ 253 │ │ _sys.audit("tempfile.mkstemp", file) │ │ 254 │ │ try: │ │ ❱ 255 │ │ │ fd = _os.open(file, flags, 0o600) │ │ 256 │ │ except FileExistsError: │ │ 257 │ │ │ continue # try again │ │ 258 │ │ except PermissionError: │ │ │ │ ╭─────────────────────────────── locals ────────────────────────────────╮ │ │ │ dir = '/home/neuro/bidsMReye/models' │ │ │ │ file = '/home/neuro/bidsMReye/models/tmpe3lsq2cm' │ │ │ │ flags = 131266 │ │ │ │ name = 'e3lsq2cm' │ │ │ │ names = <tempfile._RandomNameSequence object at 0x7f46e8840e80> │ │ │ │ output_type = <class 'str'> │ │ │ │ pre = 'tmp' │ │ │ │ seq = 0 │ │ │ │ suf = '' │ │ │ ╰───────────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ PermissionError: [Errno 13] Permission denied: '/home/neuro/bidsMReye/models/tmpe3lsq2cm' The above exception was the direct cause of the following exception: ╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮ │ /opt/miniconda-latest/envs/bidsmreye/bin/bidsmreye:8 in <module> │ │ │ │ 5 from bidsmreye.bidsmreye import cli │ │ 6 if __name__ == '__main__': │ │ 7 │ sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) │ │ ❱ 8 │ sys.exit(cli()) │ │ 9 │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ __annotations__ = {} │ │ │ │ __builtins__ = <module 'builtins' (built-in)> │ │ │ │ __cached__ = None │ │ │ │ __doc__ = None │ │ │ │ __file__ = '/opt/miniconda-latest/envs/bidsmreye/bin/bidsmreye' │ │ │ │ __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7f472cb60c40> │ │ │ │ __name__ = '__main__' │ │ │ │ __package__ = None │ │ │ │ __spec__ = None │ │ │ │ cli = <function cli at 0x7f4719f9ab80> │ │ │ │ re = <module 're' from │ │ │ │ '/opt/miniconda-latest/envs/bidsmreye/lib/python3.9/re.py'> │ │ │ │ sys = <module 'sys' (built-in)> │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/bidsmreye/bidsmreye.py:54 in │ │ cli │ │ │ │ 51 │ │ log_level = min(len(log_levels()) - 1, max(log_level + adjustment, 0)) │ │ 52 │ log_level_name = log_levels()[log_level] │ │ 53 │ │ │ ❱ 54 │ bidsmreye( │ │ 55 │ │ bids_dir=args.bids_dir, │ │ 56 │ │ output_dir=args.output_dir, │ │ 57 │ │ analysis_level=args.analysis_level, │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ args = Namespace(bids_dir='/home/neuro/data/', output_dir='/home/neuro/outputs/', │ │ │ │ analysis_level='participant', action='generalize', participant_label=None, │ │ │ │ task=None, run=None, space=None, log_level=None, debug=False, │ │ │ │ reset_database=False, bids_filter_file=None, non_linear_coreg=False, │ │ │ │ model='1to6') │ │ │ │ argv = [ │ │ │ │ │ '/opt/miniconda-latest/envs/bidsmreye/bin/bidsmreye', │ │ │ │ │ '/home/neuro/data/', │ │ │ │ │ '/home/neuro/outputs/', │ │ │ │ │ 'participant', │ │ │ │ │ '--action', │ │ │ │ │ 'generalize' │ │ │ │ ] │ │ │ │ log_level = 2 │ │ │ │ log_level_name = 'WARNING' │ │ │ │ parser = MuhParser(prog='bidsmreye', usage=None, description='BIDS app using │ │ │ │ deepMReye to decode eye motion for fMRI time series data.', │ │ │ │ formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='error', │ │ │ │ add_help=True) │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/bidsmreye/bidsmreye.py:124 in │ │ bidsmreye │ │ │ │ 121 │ log.debug(f"Configuration:\n{cfg}") │ │ 122 │ │ │ 123 │ if action in {"all", "generalize"} and isinstance(cfg.model_weights_file, str): │ │ ❱ 124 │ │ cfg.model_weights_file = download(cfg.model_weights_file) │ │ 125 │ │ │ 126 │ dispatch(analysis_level=analysis_level, action=action, cfg=cfg) │ │ 127 │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ action = 'generalize' │ │ │ │ analysis_level = 'participant' │ │ │ │ bids_dir = '/home/neuro/data/' │ │ │ │ bids_filter = None │ │ │ │ bids_filter_file = None │ │ │ │ cfg = Config( │ │ │ │ │ input_dir=PosixPath('/home/neuro/data'), │ │ │ │ │ output_dir=PosixPath('/home/neuro/outputs/bidsmreye'), │ │ │ │ │ subjects=['01'], │ │ │ │ │ space=['MNI152NLin6Asym', 'T1w'], │ │ │ │ │ task=['auditory'], │ │ │ │ │ run=[], │ │ │ │ │ model_weights_file='1to6', │ │ │ │ │ bids_filter={ │ │ │ │ │ │ 'bold': { │ │ │ │ │ │ │ 'datatype': 'func', │ │ │ │ │ │ │ 'suffix': '^bold$', │ │ │ │ │ │ │ 'extension': 'nii.*' │ │ │ │ │ │ }, │ │ │ │ │ │ 'mask': {'suffix': 'mask', 'extension': 'p'}, │ │ │ │ │ │ 'no_label': { │ │ │ │ │ │ │ 'desc': 'nolabel', │ │ │ │ │ │ │ 'suffix': '^bidsmreye$$', │ │ │ │ │ │ │ 'extension': 'npz' │ │ │ │ │ │ }, │ │ │ │ │ │ 'eyetrack': {'suffix': '^eyetrack$$', 'extension': 'tsv'}, │ │ │ │ │ │ 'eyetrack_qc': { │ │ │ │ │ │ │ 'suffix': '^eyetrack$$', │ │ │ │ │ │ │ 'extension': 'json' │ │ │ │ │ │ } │ │ │ │ │ }, │ │ │ │ │ debug=False, │ │ │ │ │ reset_database=False, │ │ │ │ │ non_linear_coreg=False │ │ │ │ ) │ │ │ │ debug = False │ │ │ │ log_level_name = 'WARNING' │ │ │ │ model_weights_file = '1to6' │ │ │ │ non_linear_coreg = False │ │ │ │ output_dir = '/home/neuro/outputs/' │ │ │ │ participant_label = None │ │ │ │ reset_database = False │ │ │ │ run = None │ │ │ │ space = None │ │ │ │ task = None │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/bidsmreye/download.py:111 in │ │ download │ │ │ │ 108 │ │ │ │ 109 │ │ file_idx = available_models().index(model_name) │ │ 110 │ │ filename = f"dataset_{available_models()[file_idx]}.h5" │ │ ❱ 111 │ │ output_file = POOCH.fetch(filename, progressbar=True) │ │ 112 │ │ if isinstance(output_file, str): │ │ 113 │ │ │ output_file = Path(output_file) │ │ 114 │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ file_idx = 7 │ │ │ │ filename = 'dataset_1to6.h5' │ │ │ │ model_name = '1to6' │ │ │ │ output_dir = PosixPath('/home/neuro/bidsMReye/models') │ │ │ │ output_file = PosixPath('/home/neuro/bidsMReye/models/dataset_1to6') │ │ │ │ POOCH = <pooch.core.Pooch object at 0x7f4719fa2340> │ │ │ │ registry_file = <_io.BufferedReader │ │ │ │ name='/opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/bids… │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/pooch/core.py:563 in fetch │ │ │ │ 560 │ │ self._assert_file_in_registry(fname) │ │ 561 │ │ │ │ 562 │ │ # Create the local data directory if it doesn't already exist │ │ ❱ 563 │ │ make_local_storage(str(self.abspath)) │ │ 564 │ │ │ │ 565 │ │ url = self.get_url(fname) │ │ 566 │ │ full_path = self.abspath / fname │ │ │ │ ╭───────────────────────── locals ──────────────────────────╮ │ │ │ downloader = None │ │ │ │ fname = 'dataset_1to6.h5' │ │ │ │ processor = None │ │ │ │ progressbar = True │ │ │ │ self = <pooch.core.Pooch object at 0x7f4719fa2340> │ │ │ ╰───────────────────────────────────────────────────────────╯ │ │ │ │ /opt/miniconda-latest/envs/bidsmreye/lib/python3.9/site-packages/pooch/utils.py:264 in │ │ make_local_storage │ │ │ │ 261 │ │ │ message.append( │ │ 262 │ │ │ │ f"Use environment variable '{env}' to specify a different location." │ │ 263 │ │ │ ) │ │ ❱ 264 │ │ raise PermissionError(" ".join(message)) from error │ │ 265 │ │ 266 │ │ 267 @contextmanager │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ action = 'write to' │ │ │ │ env = None │ │ │ │ message = [ │ │ │ │ │ "[Errno 13] Permission denied: '/home/neuro/bidsMReye/models/tmpe3lsq2cm'", │ │ │ │ │ "| Pooch could not write to data cache folder │ │ │ │ '/home/neuro/bidsMReye/models'.", │ │ │ │ │ 'Will not be able to download data files.' │ │ │ │ ] │ │ │ │ path = '/home/neuro/bidsMReye/models' │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ PermissionError: [Errno 13] Permission denied: '/home/neuro/bidsMReye/models/tmpe3lsq2cm' | Pooch could not write to data cache folder '/home/neuro/bidsMReye/models'. Will not be able to download data files.
- OS: Ventura - Matlab:2023a - SPM:12
- branch: - version: latest
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7 months ago github-actions[bot]
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7 months ago
Is there an existing issue for this?
Expected Behavior
I am trying to run an example of bidsmreye
Current Behavior
I received this permission error when using the generalize action on bidsMReye. Error says it cannot write data to cache folder.
Error message
Environment
Branch
Anything else?
No response