Creating BIDS-compatible folders and files

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: Chris Holdgraf <choldgraf@berkeley.edu>
# License: BSD (3-clause)

We’ll import the relevant functions from the write module

from mne_bids import make_bids_folders, make_bids_basename

Creating file names for BIDS

BIDS requires a specific ordering and structure for metadata fields in file paths, the function make_bids_basename 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_basename = make_bids_basename(subject='test', session='two',
                                   task='mytask', suffix='data.csv')
print(bids_basename)

Out:

sub-test_ses-two_task-mytask_data.csv

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_basename = make_bids_basename(subject='test', task='mytask')
print(bids_basename)

Out:

sub-test_task-mytask

Creating folders

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

path_folder = make_bids_folders('sub_01', session='mysession',
                                kind='meg', output_path='path/to/project',
                                make_dir=False)
print(path_folder)

# Note that passing `make_dir=True` will create the folder hierarchy, ignoring
# errors if the folder already exists.

Out:

path/to/project/sub-sub_01/ses-mysession/meg