Note
Go to the end to download the full example code.
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)
👋 Hello! This is openneuro-py 2025.1.0. Great to see you! 🤗
👉 Please report problems 🤯 and bugs 🪲 at
https://github.com/hoechenberger/openneuro-py/issues
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sub-006_task-unnamed_eeg.set: 5%|▍ | 1.86M/41.2M [00:03<00:54, 761kB/s]
sub-003_task-unnamed_eeg.set: 9%|▉ | 3.57M/39.7M [00:05<00:42, 895kB/s]
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sub-003_task-unnamed_eeg.set: 9%|▉ | 3.68M/39.7M [00:05<00:39, 946kB/s]
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sub-006_task-unnamed_eeg.set: 5%|▍ | 2.04M/41.2M [00:03<00:53, 772kB/s]
sub-003_task-unnamed_eeg.set: 10%|▉ | 3.80M/39.7M [00:05<00:40, 933kB/s]
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sub-003_task-unnamed_eeg.set: 10%|█ | 4.03M/39.7M [00:06<00:39, 956kB/s]
sub-006_task-unnamed_eeg.set: 5%|▌ | 2.22M/41.2M [00:03<00:52, 781kB/s]
sub-004_task-unnamed_eeg.set: 10%|▉ | 4.02M/42.0M [00:05<00:41, 948kB/s]
sub-003_task-unnamed_eeg.set: 10%|█ | 4.15M/39.7M [00:06<00:36, 1.01MB/s]
sub-006_task-unnamed_eeg.set: 6%|▌ | 2.31M/41.2M [00:03<00:58, 702kB/s]
sub-004_task-unnamed_eeg.set: 10%|▉ | 4.15M/42.0M [00:06<00:39, 1.00MB/s]
sub-003_task-unnamed_eeg.set: 11%|█ | 4.25M/39.7M [00:06<00:37, 984kB/s]
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sub-003_task-unnamed_eeg.set: 11%|█▏ | 4.50M/39.7M [00:06<00:34, 1.08MB/s]
sub-004_task-unnamed_eeg.set: 11%|█ | 4.48M/42.0M [00:06<00:39, 1.00MB/s]
sub-003_task-unnamed_eeg.set: 12%|█▏ | 4.61M/39.7M [00:06<00:34, 1.07MB/s]
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sub-004_task-unnamed_eeg.set: 11%|█ | 4.60M/42.0M [00:06<00:39, 997kB/s]
sub-003_task-unnamed_eeg.set: 12%|█▏ | 4.73M/39.7M [00:06<00:36, 1.01MB/s]
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sub-003_task-unnamed_eeg.set: 13%|█▎ | 5.21M/39.7M [00:07<00:33, 1.08MB/s]
sub-004_task-unnamed_eeg.set: 12%|█▏ | 5.13M/42.0M [00:07<00:36, 1.06MB/s]
sub-003_task-unnamed_eeg.set: 13%|█▎ | 5.34M/39.7M [00:07<00:33, 1.08MB/s]
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sub-003_task-unnamed_eeg.set: 14%|█▍ | 5.48M/39.7M [00:07<00:30, 1.16MB/s]
sub-004_task-unnamed_eeg.set: 13%|█▎ | 5.41M/42.0M [00:07<00:34, 1.10MB/s]
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sub-003_task-unnamed_eeg.set: 14%|█▍ | 5.59M/39.7M [00:07<00:31, 1.15MB/s]
sub-004_task-unnamed_eeg.set: 13%|█▎ | 5.56M/42.0M [00:07<00:34, 1.12MB/s]
sub-003_task-unnamed_eeg.set: 14%|█▍ | 5.73M/39.7M [00:07<00:31, 1.12MB/s]
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sub-004_task-unnamed_eeg.set: 14%|█▎ | 5.68M/42.0M [00:07<00:33, 1.14MB/s]
sub-003_task-unnamed_eeg.set: 15%|█▍ | 5.86M/39.7M [00:07<00:29, 1.19MB/s]
sub-004_task-unnamed_eeg.set: 14%|█▍ | 5.79M/42.0M [00:07<00:33, 1.14MB/s]
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sub-003_task-unnamed_eeg.set: 15%|█▌ | 5.98M/39.7M [00:07<00:30, 1.16MB/s]
sub-004_task-unnamed_eeg.set: 14%|█▍ | 5.96M/42.0M [00:07<00:31, 1.20MB/s]
sub-003_task-unnamed_eeg.set: 15%|█▌ | 6.12M/39.7M [00:08<00:29, 1.19MB/s]
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sub-003_task-unnamed_eeg.set: 16%|█▌ | 6.27M/39.7M [00:08<00:28, 1.24MB/s]
sub-004_task-unnamed_eeg.set: 15%|█▍ | 6.21M/42.0M [00:08<00:30, 1.22MB/s]
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sub-003_task-unnamed_eeg.set: 16%|█▌ | 6.41M/39.7M [00:08<00:27, 1.28MB/s]
sub-004_task-unnamed_eeg.set: 15%|█▌ | 6.39M/42.0M [00:08<00:28, 1.30MB/s]
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sub-003_task-unnamed_eeg.set: 17%|█▋ | 6.56M/39.7M [00:08<00:27, 1.27MB/s]
sub-004_task-unnamed_eeg.set: 16%|█▌ | 6.54M/42.0M [00:08<00:27, 1.33MB/s]
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sub-003_task-unnamed_eeg.set: 17%|█▋ | 6.72M/39.7M [00:08<00:25, 1.37MB/s]
sub-004_task-unnamed_eeg.set: 16%|█▌ | 6.71M/42.0M [00:08<00:25, 1.43MB/s]
sub-003_task-unnamed_eeg.set: 17%|█▋ | 6.87M/39.7M [00:08<00:24, 1.38MB/s]
sub-006_task-unnamed_eeg.set: 11%|█ | 4.43M/41.2M [00:06<00:39, 975kB/s]
sub-004_task-unnamed_eeg.set: 16%|█▋ | 6.89M/42.0M [00:08<00:24, 1.47MB/s]
sub-003_task-unnamed_eeg.set: 18%|█▊ | 7.05M/39.7M [00:08<00:23, 1.44MB/s]
sub-006_task-unnamed_eeg.set: 11%|█ | 4.60M/41.2M [00:06<00:33, 1.13MB/s]
sub-004_task-unnamed_eeg.set: 17%|█▋ | 7.05M/42.0M [00:08<00:24, 1.47MB/s]
sub-003_task-unnamed_eeg.set: 18%|█▊ | 7.22M/39.7M [00:08<00:22, 1.52MB/s]
sub-004_task-unnamed_eeg.set: 17%|█▋ | 7.24M/42.0M [00:08<00:23, 1.58MB/s]
sub-006_task-unnamed_eeg.set: 11%|█▏ | 4.71M/41.2M [00:06<00:37, 1.02MB/s]
sub-003_task-unnamed_eeg.set: 19%|█▊ | 7.40M/39.7M [00:08<00:21, 1.61MB/s]
sub-004_task-unnamed_eeg.set: 18%|█▊ | 7.44M/42.0M [00:08<00:22, 1.64MB/s]
sub-006_task-unnamed_eeg.set: 12%|█▏ | 4.86M/41.2M [00:06<00:33, 1.14MB/s]
sub-003_task-unnamed_eeg.set: 19%|█▉ | 7.57M/39.7M [00:08<00:20, 1.61MB/s]
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sub-006_task-unnamed_eeg.set: 12%|█▏ | 4.98M/41.2M [00:06<00:37, 1.02MB/s]
sub-003_task-unnamed_eeg.set: 20%|█▉ | 7.77M/39.7M [00:09<00:20, 1.66MB/s]
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sub-006_task-unnamed_eeg.set: 12%|█▏ | 5.13M/41.2M [00:06<00:33, 1.15MB/s]
sub-003_task-unnamed_eeg.set: 20%|██ | 7.98M/39.7M [00:09<00:18, 1.82MB/s]
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sub-003_task-unnamed_eeg.set: 24%|██▍ | 9.58M/39.7M [00:09<00:14, 2.25MB/s]
sub-006_task-unnamed_eeg.set: 15%|█▍ | 5.99M/41.2M [00:07<00:29, 1.25MB/s]
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sub-003_task-unnamed_eeg.set: 25%|██▍ | 9.86M/39.7M [00:10<00:12, 2.45MB/s]
sub-004_task-unnamed_eeg.set: 24%|██▍ | 9.98M/42.0M [00:10<00:13, 2.44MB/s]
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sub-003_task-unnamed_eeg.set: 25%|██▌ | 10.1M/39.7M [00:10<00:12, 2.48MB/s]
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sub-006_task-unnamed_eeg.set: 16%|█▌ | 6.49M/41.2M [00:08<00:27, 1.31MB/s]
sub-004_task-unnamed_eeg.set: 26%|██▌ | 10.8M/42.0M [00:10<00:12, 2.71MB/s]
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sub-003_task-unnamed_eeg.set: 28%|██▊ | 11.3M/39.7M [00:10<00:10, 2.89MB/s]
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sub-003_task-unnamed_eeg.set: 30%|███ | 11.9M/39.7M [00:10<00:09, 2.93MB/s]
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sub-003_task-unnamed_eeg.set: 31%|███ | 12.3M/39.7M [00:10<00:08, 3.27MB/s]
sub-004_task-unnamed_eeg.set: 30%|██▉ | 12.5M/42.0M [00:10<00:09, 3.38MB/s]
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sub-006_task-unnamed_eeg.set: 19%|█▉ | 7.78M/41.2M [00:09<00:23, 1.50MB/s]
sub-003_task-unnamed_eeg.set: 35%|███▍ | 13.9M/39.7M [00:11<00:07, 3.75MB/s]
sub-004_task-unnamed_eeg.set: 34%|███▎ | 14.1M/42.0M [00:11<00:07, 3.91MB/s]
sub-006_task-unnamed_eeg.set: 19%|█▉ | 8.03M/41.2M [00:09<00:19, 1.77MB/s]
sub-003_task-unnamed_eeg.set: 36%|███▌ | 14.3M/39.7M [00:11<00:06, 3.87MB/s]
sub-004_task-unnamed_eeg.set: 34%|███▍ | 14.5M/42.0M [00:11<00:07, 3.81MB/s]
sub-003_task-unnamed_eeg.set: 37%|███▋ | 14.7M/39.7M [00:11<00:06, 3.94MB/s]
sub-006_task-unnamed_eeg.set: 20%|██ | 8.25M/41.2M [00:09<00:20, 1.67MB/s]
sub-004_task-unnamed_eeg.set: 36%|███▌ | 14.9M/42.0M [00:11<00:07, 3.98MB/s]
sub-006_task-unnamed_eeg.set: 21%|██ | 8.48M/41.2M [00:09<00:18, 1.85MB/s]
sub-003_task-unnamed_eeg.set: 38%|███▊ | 15.1M/39.7M [00:11<00:06, 3.80MB/s]
sub-004_task-unnamed_eeg.set: 37%|███▋ | 15.4M/42.0M [00:11<00:06, 4.16MB/s]
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✅ Finished downloading ds004745.
🧠 Please enjoy your brains.
Now, loading the dataset is simply a one-line command:
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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)
/Users/baristim/Projects/braindecode-1/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 29.469 seconds)
Estimated memory usage: 771 MB