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

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1

Ahoi hoi everyone,

Iā€™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, Iā€™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 ā€œproblemā€ 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 yā€™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, youā€™ve come to the right place! :phone: :smile:

@PeerHerholz
I will have a look later today, shouldnā€™t be too hard to get this to work! Iā€™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 thereā€™s anything I can do to help.

Cheers, Peer

5

I have opened a pull request:

Fancy checking if this branch solves the issue for you?

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

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thx @richard for the fast fix, thatā€™s amazing! Iā€™ll check it asap and report back!

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