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OpenNeuroOrg / openneuro

A free and open platform for analyzing and sharing neuroimaging data
https://openneuro.org/
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bids validation hanging on ds005123? #3108

Open DVSneuro opened 2 months ago

DVSneuro commented 2 months ago

What went wrong?

The BIDS validation step has running for over 24 hours on ds005123. Is it hanging? We never got it to complete before the snapshot was published, but we have confirmed locally that the dataset is valid.

Expected behavior

We expected the bids validation step to complete within a few minutes (or at least a few hours).

How to reproduce

  1. Go to https://openneuro.org/datasets/ds005123/versions/1.1.0
  2. Observe validation running (for 24+ hours)

Desktop

Phone

Additional information

Our dataset might be a little larger than others. We have noticed locally that it fails the validation step if we do not include the --ignoreNiftiHeaders option as below:

singularity run --cleanenv -B /home/tug87422/work/rf1-dwi/bids:/data ~/work/tools/bids-validator-v1.14.6.sif /data --verbose --ignoreWarnings --ignoreNiftiHeaders --ignoreSubjectConsistency

I wonder if OpenNeuro could include options for the bids validation step? The --ignoreNiftiHeaders option seems to be critical with large datasets.

Thanks for any help!

David

DVSneuro commented 2 months ago

Update: we made some additional changes to this dataset, published a new snapshot, and the validation completed. I am not sure why it was hanging initially, though, so I'm leaving this as an open issue. Thanks!