Error running MRIQC

1

Hi all,

I’m experiencing some issues when running mriqc with Docker, it seems like it does not recognize the folder as bids, but the BIDS validator (I used the online version) doesn’t give me any error.

Here is the error I receive:

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/mriqc", line 11, in <module>
    load_entry_point('mriqc==0.11.0', 'console_scripts', 'mriqc')()
  File "/usr/local/miniconda/lib/python3.6/site-packages/mriqc/bin/mriqc_run.py", line 283, in main
    task=opts.task_id,
  File "/usr/local/miniconda/lib/python3.6/site-packages/mriqc/utils/bids.py", line 24, in collect_bids_data
    layout = BIDSLayout(dataset)
  File "/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py", line 315, in __call__
    **kwargs)
  File "/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/bids_layout.py", line 103, in __init__
    exclude=exclude, **kwargs)
  File "/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py", line 418, in __init__
    self._load_domain(c, root, True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/grabbit/core.py", line 461, in _load_domain
    "exist!" % (root, config['name']))
ValueError: Root directory /media/DATA1/TestControl for domain bids does not exist!

I checked the folder several times, paths and content are correct. Any suggestion on what could be wrong here?

Thank you so much!

Best,

Giulia

2

I ran into a similar issue when using a singularity container for mriqc. It turned out I just needed to mount the relevant local directories. https://singularity.lbl.gov/docs-mount

/media/ does not seem like a typical system defined path that might be automatically mounted. Maybe you are running into a similar issue.

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