bids.layout cannot index anat data from openneuro ds000114-fmriprep

[Remi-Gau]

in datalad super dataset:

datasets.datalad.org/openneuro-derivatives/ds000114-fmriprep

anat data from the 2 sessions was averaged and into a single anat folder and this breaks the expectation of bids.layout

sub-01
├── anat
├── figures
├── log
│   └── 20220619-170623_dd955994-7a1e-4d66-a6af-a23c3ea1838a
├── ses-retest
│   ├── anat
│   └── func
└── ses-test
    ├── anat
    └── func

>> bids.query(layout, 'data', 'sub' ,'01', 'modality', 'anat')
ans =
  2×1 cell array
    {'/home/remi/github/cpp-lln-lab/bidspm/lib/bids-matlab/tmp/ds000114-fmriprep/sub-01/ses-retest/anat/sub-01_ses-retest_from-orig_to-T1w_mode-image_xfm.txt'}
    {'/home/remi/github/cpp-lln-lab/bidspm/lib/bids-matlab/tmp/ds000114-fmriprep/sub-01/ses-test/anat/sub-01_ses-test_from-orig_to-T1w_mode-image_xfm.txt'    }

[Remi-Gau]

Current structure of the layout is this

  %% BIDS structure
  % ==========================================================================
  % BIDS.pth           -- BIDS directory
  % BIDS.is_datalad_ds -- BIDS directory
  % BIDS.description   -- content of dataset_description.json
  % BIDS.sessions      -- cellstr of sessions
  % BIDS.participants  -- for participants.tsv
  % BIDS.phenotype     -- for content of the phenotype folder
  % BIDS.subjects      -- structure array of subjects
  % BIDS.root          -- tsv and json files in the root folder

With BIDS.subjects(2) being subject 1 session 2 if the dataset has sessions, but is subject 2 if the dataset has no session level folders.

Currently we do not expect datatype folders at the same level as the session folder.