11. Creating BIDS-compatible folder names and filenames

The Brain Imaging Data Structure (BIDS) has standard conventions for file names and folder hierarchy. MNE-BIDS comes with convenience functions if you wish to create these files/folders on your own.

Note

You may automatically convert Raw objects to BIDS-compatible files with write_raw_bids. This example is for manually creating files/folders.

# Authors: The MNE-BIDS developers
# SPDX-License-Identifier: BSD-3-Clause

First we will import the relevant functions

import shutil

import mne

from mne_bids import BIDSPath

Creating file names for BIDS

BIDS requires a specific ordering and structure for metadata fields in file paths, the class BIDSPath allows you to specify many such pieces of metadata, ensuring that they are in the correct order in the final file path. Omitted keys will not be included in the file path.

bids_path = BIDSPath(
    subject="test", session="two", task="mytask", suffix="events", extension=".tsv"
)
print(bids_path)

sub-test/ses-two/sub-test_ses-two_task-mytask_events.tsv

You may also omit the suffix, which will result in only a prefix for a file name. This could then prepended to many more files.

bids_path = BIDSPath(subject="test", task="mytask")
print(bids_path)

sub-test/sub-test_task-mytask

Creating folders

You can also use MNE-BIDS to create folder hierarchies.

my_root = mne.datasets.sample.data_path()  # replace with *your* root folder
bids_path = BIDSPath(
    subject="mneBIDStest", session="mysession", datatype="meg", root=my_root
).mkdir()
print(bids_path.directory)

# clean up
shutil.rmtree(my_root / "sub-mneBIDStest")

/home/circleci/mne_data/MNE-sample-data/sub-mneBIDStest/ses-mysession/meg