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`niworkflows.utils.bids.collect_data` failing to retrieve BOLD images #293

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oesteban opened this Issue Jan 28, 2019 · 4 comments

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oesteban commented Jan 28, 2019

It seems that the original bug causing poldracklab/fmriprep#1481 is still there (https://neurostars.org/t/fmriprep-from-singularity-unboundlocalerror/3299/9?u=oesteban).

Not getting a 'bold' entry after the BIDSLayout query would explain the original UnboundLocalError symptom. @emdupre first noticed this during #285.

@effigies, any quick thoughts about what could've changed in pybids land that we did not account for in our end?

@oesteban oesteban added the bug label Jan 28, 2019

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effigies commented Jan 28, 2019

We're still depending on pybids 0.6.5... Nothing has changed in that. Unless there's some reason that 0.7.0 is getting pulled in?

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oesteban commented Jan 28, 2019

@emdupre could not replicate the original bug, and the error seems persistent only with singularity containers. Maybe a system-wide installation pybids installation is coming into play.

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effigies commented Jan 28, 2019

That's a thought I had, but the paths in their tracebacks are in the same directory as fmriprep.

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effigies commented Jan 28, 2019

Perhaps their singularity image is at fault. Do we have one we can verify works on our data, and give to them to see if they still reproduce the failure?

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