Naming convention in mne vs. mne-bids: welcome to the thunderdome (?)

Ahoi hoi everyone,

I’m currently trying to streamline my preprocessing/analyses via a pipeline and came across a question concerning the naming conventions in mne vs. mne-bids (or rather BIDS in general).

I start from .bdf files which I convert to BIDS conform files via mne-bids, resulting in .eeg, .vhdr and .vmrk files for a given .bdf file. This step works fine as I can successfully run the bids-validator, use pybids to query the dataset and use mne-bids to read in files. Now I want to use reports (report.parse_folder) to create a barebones report following this example. However, as defined in reports.py

VALID_EXTENSIONS = ['raw.fif', 'raw.fif.gz', 'sss.fif', 'sss.fif.gz']

mne naming conventions indicate *raw.fif and thus specifying pattern='*.vhdr' results in an error stating No matching files found .... In subsequent analyses, I’m converting and saving the files as .fif. However, so far only after filtering, etc. .
It seems that in order to include raw (as in unprocessed) data, I would need to save files as .fif after reading them via mne-bids which would create an additional file.
The same “problem” might occur further down the processing pipeline, as BIDS derivatives (so far in general as only common derivatives are merged and M/(s)EEG derivatives might be adapted correspondingly) and mne naming conventions will diverge again.

Do y’all have any idea/input regarding this? Sorry if I missed this discussion elsewhere. Brashly tagging @sappelhoff and @richard.

Cheers, Peer

P.S.:

  • MNE-Python version: 0.22.0
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we should add support for more than fif files in the report

I am sure @richard can help

Alex

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Thanks for calling our hotline, you’ve come to the right place! :phone: :grinning_face_with_smiling_eyes:

@PeerHerholz
I will have a look later today, shouldn’t be too hard to get this to work! I’ll keep you posted. Thanks for raising this issue!

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Hi @agramfort and @richard,

thank you very much for the fast response and support.
Please let me know if there’s anything I can do to help.

Cheers, Peer

I have opened a pull request:

Fancy checking if this branch solves the issue for you?

This should work now with the latest development version, and will be included in the 0.23 release of MNE-Python.

thx @richard for the fast fix, that’s amazing! I’ll check it asap and report back!

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