Fail to capture all EEG files and wrong number of subjects

[arnodelorme]

Only capture the raw data, channel and event file. Misses the JSON files.
Also, there are only 2 subjects (with 3 sessions each). Yet the program think there are 6 subjects

[Remi-Gau]

hey @arnodelorme

Try to use bids.query to access specific pieces of information of the layout. This is how the whole thing has been designed. 😉

I still need to write some sort of official doc on this but in the mean time you can look at test_bids_query as a source of unofficial doc.

In your case, what do the following give you?

bids.query(res, 'subjects')
bids.query(res, 'data', 'sub', '01')

Also I am pretty sure that JSON files are not "indexed". Am I right @gllmflndn?

If you want to get the content of some JSON file you would need to do something like this:

bids.query(res, 'metadata', 'sub', '01', 'task', 'Experiment')

[arnodelorme]

Why not load it all?

[Remi-Gau]

Not sure why that initial decision was made though I suspect that this in part related to dealing with the inheritance principle which implies that the metadata about a given file could be spread in several JSON, so this is dealt with on the fly when metadata is requested.

[Remi-Gau]

hey @arnodelorme

PR #47 should be able to index the json files that are in any "modality" folder a subject if you ask for a schema-less layout.

use_schema = true();
BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_rishikesh'), use_schema);
bids.query(BIDS, 'data', 'sub', '001', 'ses', '01')

ans =

  3×1 cell array

    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_channels.tsv'
    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_eeg.bdf'
    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_events.tsv'

%%
use_schema = false();
BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_rishikesh'), use_schema);
bids.query(BIDS, 'data', 'sub', '001', 'ses', '01')

ans =

  4×1 cell array

    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_channels.tsv'
    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_eeg.bdf'
    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_eeg.json'
    'bids-examples/eeg_rishikesh/sub-001/ses-01/eeg/sub-001_ses-01_task-meditation_events.tsv'

I have shortened the full path in the copy-paste to make it easier to read.

Will merge the PR in the dev branch

[arnodelorme]

Thank you