Problem

Currently in the standard, there is this notion of a modality, which I totally assumed meant eeg, meg, ieeg, anat, etc. So therefore they would be the "modality" directories that followed subject and session. For example:

sub-01/ses-01/<modality>/

However, there is also a modality entity which is primarily used in anat sub-directories to differentiate various imaging modalities. This shows up like sub-01/ses-01/anat/sub-01_ses-01_mod-T2w_defacemask.nii.gz.

Anat using modality in different ways:
https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#anatomy-imaging-data

Entity table:
https://bids-specification.readthedocs.io/en/stable/99-appendices/04-entity-table.html

Expectation

It would be helpful to have the specification explicitly define what to call the directory level names vs. the filename specific modality entity. Since calling them both modality leads to a bit of confusion since there is no good 1-1 matching.

Idk what's the right answer here so would be helpful to get some thoughts and then I can PR if it's feasible :p.

Additional Info

See a problem that surfaced in mne-bids at: mne-tools/mne-bids#519 (comment)

cc @jasmainak @sappelhoff @hoechenberger @agramfort