Error in BIDSPath while reading openneuro BIDs

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#1

**:question: Errors with read_raw_bids with .edf files

  • MNE version:
    mne==0.24.1
    mne-bids==0.9

  • operating system: Manjaro 21.2.0

Hello there!
Iā€™m having a problem with .set files in a dataset found in the OpenNeuro repository.
Now I am testing the ds003774 dataset, and itā€™s not getting the correct BIDSPath.
I guess itā€™s getting the session variable into the run variable; again, itā€™s a guess.
The code is the following:

BIDSPath

Thanks again guys

Best regards

#2

Hello @AngelicaRibeiro,

I didnā€™t have time to look at your code in detail, but I quickly cooked up the following MWE:

# %%
from pathlib import Path
import openneuro
import mne_bids


bids_root = Path('/tmp/ds003774')

# %%
openneuro.download(
    dataset='ds003774',
    target_dir=bids_root,
    include=['sub-001']
)

# %%
bids_path = mne_bids.BIDSPath(
    subject='001',
    session='01',
    task='MusicListening',
    run='1',
    suffix='eeg',
    extension='.set',
    datatype='eeg',
    root=bids_root
)
raw = mne_bids.read_raw_bids(bids_path=bids_path)
print(raw)

This seems to work, although Iā€™m getting quite a number of warnings:

Reading events from /tmp/ds003774/sub-001/ses-01/eeg/sub-001_ses-01_task-MusicListening_run-1_events.tsv.
Reading channel info from /tmp/ds003774/sub-001/ses-01/eeg/sub-001_ses-01_task-MusicListening_run-1_channels.tsv.
Reading in coordinate system frame Other: None.
<RawEEGLAB | sub-001_ses-01_task-MusicListening_run-1_eeg.set, 129 x 34009 (136.0 s), ~33.6 MB, data loaded>
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:59: RuntimeWarning: Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
raw = reader[ext](raw_path, **kwargs)
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:59: RuntimeWarning: Omitted 106 annotation(s) that were outside data range.
raw = reader[ext](raw_path, **kwargs)
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:59: RuntimeWarning: Limited 2 annotation(s) that were expanding outside the data range.
raw = reader[ext](raw_path, **kwargs)
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:59: RuntimeWarning: The data contains ā€˜boundaryā€™ events, indicating data discontinuities. Be cautious of filtering and epoching around these events.
raw = reader[ext](raw_path, **kwargs)
/Users/hoechenberger/Development/mne-bids/mne_bids/dig.py:502: RuntimeWarning: EEG Coordinate frame is not accepted BIDS keyword. The allowed keywords are: [ā€˜ACPCā€™, ā€˜Pixelsā€™, ā€˜Otherā€™]
warn(ā€œEEG Coordinate frame is not accepted "
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:754: RuntimeWarning: participants.tsv file not found for /tmp/ds003774/sub-001/ses-01/eeg/sub-001_ses-01_task-MusicListening_run-1_eeg.set
warn(f"participants.tsv file not found for {raw_path}ā€)

@sappelhoff this really doesnā€™t look great, eh??

#3

mmh can maybe take a deeper look soon, but we should make mne-bids aware of the EEGLAB and EEGLAB-HJ coordinate frames, which are newly supported: Coordinate systems - Brain Imaging Data Structure v1.6.1-dev

#4

okay, the EEGLAB and EEGLAB-HJ coordsystems werenā€™t even the issue. (Iā€™ll still open an issue on mne-bids that we try to handle those, because new versions of EEGLAB-BIDS write these keywords to coordsystem.json).

Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
raw = reader[ext](raw_path, **kwargs)

This issue comes from MNE-Python ā€¦ we can address it in mne-bids by setting preload for .set to True always.

The boundary events warning is fair

the warning about omitted and/or limited annotations is worrying, thatā€™s something Iā€™d be grateful if you, @AngelicaRibeiro, could investigate further and alert us if itā€™s a problem with mne-bids or mne-python

Iā€™ll open a couple of issues on mne-bids. But for more than that I donā€™t have time right now :slight_smile:

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