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-bids (or rather
BIDS in general).
I start from
.bdf files which I convert to
BIDS conform files via
mne-bids, resulting in
.vmrk files for a given
.bdf file. This step works fine as I can successfully run the
pybids to query the dataset and use
mne-bids to read in files. Now I want to use
report.parse_folder) to create a barebones report following this example. However, as defined in
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.
- MNE-Python version: 0.22.0