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Description
Problem:
bids.layout.BIDSlayout also includes files from the sourcedata folder.
Example:
The top folder of my BIDS dataset looks like this:
ROOT='D:/BIDS_pilot'
layout=bids.BIDSLayout(ROOT)
#get all subjects
layout.get_subjects()
This returns
['82', '88', '91', '95', '003', '004', '005', '006']
Which is a little confusing, given that there's clearly only 1 subject folder (and only one subject listed in participants.tsv).
However, asking for all files from subject 82:
#get all files from subject 82:
layout.get(subject='82')
[<BIDSDataFile filename='D:\BIDS_pilot\sourcedata\Sub001\lab\ASSRParadigm\sub-82_ASSRParadigm-behavioral-data_1730798988.tsv'>,
<BIDSFile filename='D:\BIDS_pilot\sourcedata\Sub001\lab\ASSRParadigm\sub-82_ASSRParadigm-EyeTracking_1730798988.edf'>,
<BIDSDataFile filename='D:\BIDS_pilot\sourcedata\Sub001\lab\SetupParadigm\sub-82_SetupParadigm-behavioral-data_1730798988.tsv'>,
<BIDSFile filename='D:\BIDS_pilot\sourcedata\Sub001\lab\SetupParadigm\sub-82_SetupParadigm-EyeTracking_1730798988.edf'>,
<BIDSDataFile filename='D:\BIDS_pilot\sourcedata\Sub001\lab\sub-82_events_1730798988.tsv'>,
<BIDSFile filename='D:\BIDS_pilot\sourcedata\Sub001\lab\sub-82_ParadigmRunner-log_1730798988.log'>]
But, the documentation says that "By default, indexing ignores all files in 'code/', 'stimuli/', 'sourcedata/', 'models/', and any hidden files/dirs beginning with '.' at root level."
So what is likely to be the issue?
I am using pybids 0.18.1 on windows.