IndexError: list index out of range

[giulia-berto]

Hi, I'm trying to run the first-level analysis through docker/singularity after having run fMRIPrep on sub-10 of this dataset. The command I am running is the following:

singularity run \
    -B `pwd`/bids:/bids \
    -B `pwd`/${derdir}:/derivatives_dir \
    -B `pwd`/${outdir}:/output \
    -B `pwd`/${workdir}:/work \
    docker://poldracklab/ds003-example:0.0.3 \
    /derivatives_dir /output participant \
    --participant-label $sub \
    --work-dir work \
    --bids-dir /bids \
    --space MNI152NLin2009cAsym 

where output and work are two empty directories that I created. However, I get the following error:

INFO:    Using cached SIF image
Failed to import duecredit due to No module named 'duecredit'
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  from collections import Container
Traceback (most recent call last):
  File "/src/run.py", line 180, in <module>
    sys.exit(main())
  File "/src/run.py", line 153, in main
    suffix='events', return_type='file', **subquery)[0]
IndexError: list index out of range

Any suggestions on how to handle this? Thank you!

EDIT: this happens both when running fMRIPrep by myself and when using the data already pre-processed found here: https://datasets.datalad.org/?dir=/labs/poldrack/ds003_fmriprep

[oesteban]

Hi @giulia-berto,

I'm very unclear about what could be the cause for this problem (pinging @rciric), but

• at first it looks like the container image is a bit outdated - your error message complains about line 153 but the actual line is currently 163

  ds003-post-fMRIPrep-analysis/run.py

  Lines 163 to 164 in e300357

  	inputs[sub]['events'] = layout.get(
  	suffix='events', return_type='file', **subquery)[0]

• it seems that the image is complaining about missing events files - are they found under /bids ?

[giulia-berto]

Hi @oesteban, yes, I do have the events in the bids folder under bids/sub-10/func/sub-10_task-rhymejudgment_events.tsv