fMRIPrep via singularity

1

Hi,

I’m trying to run fmriprep on a HPC using slurm and singularity but I’m experiencing the following error:
/opt/conda/lib/python3.8/site-packages/bids/config.py:39: FutureWarning: Setting ‘extension_initial_dot’ will be removed in pybids 0.16.
warnings.warn(“Setting ‘extension_initial_dot’ will be removed in pybids 0.16.”,
Traceback (most recent call last):
File “/opt/conda/bin/fmriprep”, line 8, in
sys.exit(main())
File “/opt/conda/lib/python3.8/site-packages/fmriprep/cli/run.py”, line 42, in main
import sentry_sdk
File “”, line 991, in _find_and_load
File “”, line 975, in _find_and_load_unlocked
File “”, line 671, in _load_unlocked
File “”, line 844, in exec_module
File “”, line 980, in get_code
File “”, line 1038, in get_data
OSError: [Errno 5] Input/output error

Has anyone else had this issue and/or have any suggestions on how to resolve this?

Thanks in advance,
Phoenix

2

May you please provide the following information:

  1. What version fMRIPrep are you using (if not most recent, 21.0.0, consider upgrading)?
  2. Is your dataset BIDS valid (if not, work to fix validation errors)?
  3. Please paste the command you used to run fMRIPrep (or something close to it, if you don’t want us to see the names of file paths)
  4. Is this error subject specific?

Steven

3

Hi Steven,

Thanks for your prompt response!

  1. I’m using the most recent version of fMRIPrep
  2. My dataset is BIDS valid
  3. I am running fMRIPrep using the py script found here: https://github.com/N-HEDGER/NEURO_PYTHON/tree/master/FMRIPREP_SINGULARITY_SLURM/scripts - as the script is very large let me know if there’s any specific sections you want to see of my script.
  4. This error occurs for all subjects

Thanks again,
Phoenix

4

The code you linked to makes a job script. It would help to see what the job script looks like. My guess based on the error message is that an important path for fmriprep is either not being passed into singulairty correctly or is not mounted in the singularity container.