File hierarchy is unclear : location of “raw data” / “BIDS-managed data”?

[DimitriPapadopoulos]

I may be wrong but the standard is unclear or not clear enough about the location of NIfTI “raw data” or “BIDS-managed data”.

I understand:

• We store source data such as DICOM files in subfolder sourcedata.
• We store processed data such as normalized NIfTI files in derivatives.
  This is explained in Common principles | Source vs. raw vs. derived data:

BIDS in its current form is designed to harmonize and describe raw (unprocessed or minimally processed due to file format conversion) data. During analysis such data will be transformed and partial as well as final results will be saved. Derivatives of the raw data (other than products of DICOM to NIfTI conversion) MUST be kept separate from the raw data. This way one can protect the raw data from accidental changes by file permissions. In addition it is easy to distinguish partial results from the raw data and share the latter. Similar rules apply to source data which is defined as data before harmonization and/or file format conversion (for example E-Prime event logs or DICOM files).

However it is unclear where we should store the sub-<label> subfolders with the raw NIfTI files. Directly under the root folder of the dataset?

If so, Directory structure | Single session example is misaligned and thus misleading:

sub-control01/
    anat/
    .
    .
    .
    code/
        deface.py
    derivatives/
    README
    participants.tsv
    dataset_description.json
    CHANGES