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
