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UNFmontreal / Dcm2Bids

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
https://UNFmontreal.github.io/Dcm2Bids/
GNU General Public License v3.0
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apptainer / singularity version requirement #323

Open celstark opened 6 days ago

celstark commented 6 days ago

Running your container in apptainer 1.3.4 is just fine. Running it in 1.2.5 (or older versions of singularity) gives the following:

apptainer --version
apptainer version 1.2.5-1.el9

apptainer exec code/dcm2bids_3.2.0.sif dcm2bids --help
Traceback (most recent call last):
  File "/venv/bin/dcm2bids", line 5, in <module>
    from dcm2bids.cli.dcm2bids import main
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1322, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1262, in _find_spec
  File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 20, in find_spec
    return cls._find_spec(fullname, Path(pkg_path))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.12/site-packages/__editable___dcm2bids_3_2_0_finder.py", line 38, in _find_spec
    if candidate.exists():
       ^^^^^^^^^^^^^^^^^^
  File "/venv/lib/python3.12/pathlib.py", line 860, in exists
    self.stat(follow_symlinks=follow_symlinks)
  File "/venv/lib/python3.12/pathlib.py", line 840, in stat
    return os.stat(self, follow_symlinks=follow_symlinks)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied: '/dcm2bids/dcm2bids/__init__.py'

The prior 3.1.0 though was fine:

apptainer exec code/dcm2bids_3.1.0.sif dcm2bids --help
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR] [--auto_extract_entities] [--bids_validate]
                [--force_dcm2bids] [--skip_dcm2niix] [--clobber] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

options:
  -h, --help            show this help message and exit
...

Note, it does run in the newer apptainer:

apptainer --version
apptainer version 1.3.4-1.el9

apptainer exec code/dcm2bids_3.1.0.sif dcm2bids --help
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR] [--auto_extract_entities] [--bids_validate]
                [--force_dcm2bids] [--skip_dcm2niix] [--clobber] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v]

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

options:
  -h, --help            show this help message and exit
...
arnaudbore commented 2 days ago

Thank you for the issue. I will check if I can make it work otherwise I will need to tell people to update apptainer.