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BIDS Dataset Example#

In this example, we show how to fetch and prepare a BIDS dataset for usage with Braindecode.

# Authors: Pierre Guetschel <pierre.guetschel@gmail.com>
#
# License: BSD (3-clause)

from pathlib import Path

import openneuro

from braindecode.datasets import BIDSDataset

First, we download a collection of (fake/empty) BIDS datasets.

# import tempfile
# data_dir = tempfile.mkdtemp()
data_dir = Path("~/mne_data/openneuro/").expanduser()
dataset_name = "ds004745"  # 200Mb dataset
dataset_root = data_dir / dataset_name

if not dataset_root.exists():
    openneuro.download(dataset=dataset_name, target_dir=dataset_root)

Now, loading the dataset is simply a one-line command:

bids_ds = BIDSDataset(dataset_root)

/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "1" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "2" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "3" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "4" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "5" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "6" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "7" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "8" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "1" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "2" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "3" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "4" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "5" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "6" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "7" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "8" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "1" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "2" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "3" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "4" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "5" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "6" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "7" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "8" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "1" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "2" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "3" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "4" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "5" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "6" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "7" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "8" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "1" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "2" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "3" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "4" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "5" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "6" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "7" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)
/home/runner/work/braindecode/braindecode/braindecode/datasets/bids.py:191: RuntimeWarning: No BIDS -> MNE mapping found for channel type "n/a". Type of channel "8" will be set to "misc".
  raw = mne_bids.read_raw_bids(bids_path, verbose=False)

And we can see that the events of this dataset are set in the .annotations attribute of the raw data:

print(bids_ds.datasets[0].raw.annotations)

<Annotations | 58 segments: 1 (6), 10 (10), 2 (6), 3 (6), 4 (6), 5 (6), 6 ...>

Total running time of the script: (0 minutes 1.376 seconds)

Estimated memory usage: 1215 MB

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