I want to index a bids dataset and a specific derivatives directory in a single layout.
(And I want to do it in a way that’s considered best practice)
What is the “correct” way to index a bids dataset and a derivatives dataset?
My Current Solution
from bids.layout import BIDSLayout bids_dir = '/home/james/test/BetterDirectoryStructure/3-Experiment/2-data/bids' deriv_dir = '/home/james/test/BetterDirectoryStructure/3-Experiment/2-data/bids/derivatives/fmriprep' lay = BIDSLayout([(bids_dir, ['bids']), (deriv_dir, ['bids', 'derivatives'])], include='sub-*')
Note: I used
include='sub-*' as a general way to ignore other folders and only collect the subject specific information (this will not be applicable for all derivatives, but it is useful for my application). Is it doing what I expect (e.g. only checking the root level directory for folders/files that match the
sub-* regex)? Rambling on, I should probably also include a
*.json entry to include top level jsons.