How to find non-BIDS data

In some cases you might want to use a dataset that is not (entirely) BIDS compatible. While UnfoldBIDS.jl is expecting you to comply with the BIDS structure, you can also make use of the underlying functions to (at least) find your data.

The key element here is that a lot of what bids_layout() is doing, is to find the right data based on your input. However, you can also do that manually, by using UnfoldBIDS.list_all_paths() The function takes in a few keywords:

UnfoldBIDS.list_all_paths(path, file_ending, file_pattern; exclude=nothing)

Where

path::String = path_to_data_folder; should be input with abspath()
file_ending::String = data_file_ending; UnfoldBIDS is looking for file_ending = [".set", ".fif", ".vhdr", ".edf"], but maybe you are looking for a ".mat"?
file_pattern::String = ses_task_run; this control for which session/task/run you are looking for (e.g. "ses-001"); can be empty String to look for everything: file_pattern = [""]
exclude = folder_to_exclude; If there is a folder in your pathtodata_folder you want to exclude you can input this here; defaults to nothing

In an applied case you would then:

# Init a files DataFrame
files_df = DataFrame(subject=[], ses=[], task=[], run=[], file=[])  # Initialize an empty DataFrame to hold results

# path settings
bidsPath = "path/to/folder"
file_ending = [".mat"]
file_pattern = [""]
exclude = nothing

# Find paths
all_paths = collect(list_all_paths(abspath(bidsPath), file_ending, file_pattern, exclude=exclude))

Note

It is not tested whether you can find data that is stored in a different way than BIDS structured (e.g. all files in one folder instead of one sub-XXX folder per subject); but technically this should be possible.

Additionally you want to put your found paths in a nicer DataFrame containing subject specific information

# Init a files DataFrame
files_df = DataFrame(subject=[], ses=[], task=[], run=[], file=[])  # Initialize an empty DataFrame to hold results

# Add subject information
for path in all_paths
    UnfoldBIDS.extract_subject_id!(files_df, path)
end

# Check for multiple session/tasks/runs
ses = nothing; task = nothing; run = nothing;
UnfoldBIDS.check_df(files_df, ses, task, run)

Note

This does not look for your events; and if you used a different file ending than UnfoldBIDS' default you won't be able to use load_bids_eeg_data with your DataFrame!

This page was generated using Literate.jl.