Fieldmaps do not find metadata when part-{mag,phase} are present and a single sidecar is given

[oesteban]

I have:

sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_epi.json
sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_part-mag_epi.nii.gz
sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_part-phase_epi.nii.gz

I would expect that get_metadata (or access the metadata member, whatever is the current way of accessing it) for either the magnitude or the phase would retrieve the metadata from the common json sidecar.

I would also expect higher-level metadata be extracted from /acq-bold_epi.json, in this case.

[oesteban]

Or did I misunderstand the BIDS specs, @effigies ?

[effigies]

I would expect inheritance to apply here.

[oesteban]

I would expect inheritance to apply here.

So, to be clear, you would expect that the metadata in /sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_epi.json and /acq-bold_epi.json both apply?

[Remi-Gau]

yes though those from /sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_epi.json would override any from /acq-bold_epi.json

[oesteban]

Thanks.

For a start skimming the code, ext_key is undefined here:

pybids/bids/layout/index.py

Lines 268 to 272 in 8fb92fa

	if filters.get(ext_key):
	filters[ext_key] = listify(filters[ext_key])
	# ensure json files are being indexed
	if '.json' not in filters[ext_key]:
	filters[ext_key].append('.json')

[oesteban]

Okay, false alarm -- I was using an old version of the command line without --index-metadata. This indeed works, so I'm closing. The undefined variable is there though, should I open an issue?

[effigies]

Yeah. Looks like the definition was removed in b1140ee. ext_key should just become 'extension'.