Loading collections fails when derivatives is outside parent directory #383
Description
If layout is set up as such:
layout = BIDSLayout('/bids', derivatives='/fmriprep')
Then the following will fails
layout.get_collections()
because the TR for an image in the derivatives can't be found:
~/repos/pybids/bids/variables/io.py in load_variables(layout, types, levels, skip_empty, dataset, **kwargs)
74 _kwargs = kwargs.copy()
75 _kwargs.update(type_flags)
---> 76 dataset = _load_time_variables(layout, dataset, **_kwargs)
77
78 for t in ({'scans', 'sessions', 'participants'} & set(types)):
~/repos/pybids/bids/variables/io.py in _load_time_variables(layout, dataset, columns, scan_length, drop_na, events, physio, stim, regressors, skip_empty, **selectors)
160
161 tr = layout.get_metadata(img_f, suffix='bold', domains=domains,
--> 162 full_search=True)['RepetitionTime']
163
164 run = dataset.get_or_create_node('run', entities, image_file=img_f,
KeyError: 'RepetitionTime'
If I instead add a symlink to derivatives/fmriprep then it works.
This might be a more general issue of how meta-data is searched when the root folder differs.