moabb.datasets.Perdikis2018#

class moabb.datasets.Perdikis2018[source]#

Bases: BaseDataset

[source]

Dataset Snapshot

Perdikis2018

EEG recordings and application logs from the two tetraplegic pilots of team Brain Tweakers (CNBI, EPFL) during longitudinal motor-imagery BCI training and the Cybathlon 2016 BCI race; this loader exposes the cue-based offline calibration runs (both-hands / both-feet / rest).

Imagery, 3 classes (both_feet vs both_hands vs rest)

AuthorsSerafeim Perdikis, Luca Tonin, Sareh Saeedi, Christoph Schneider, Jose del R. Millan

🇨🇭 Defitech Chair in Brain-Machine Interface (CNBI), Center for Neuroprosthetics, Ecole Polytechnique Federale de Lausanne (EPFL), CH·2018
Imagery Code: Perdikis2018 2 subjects 1 session 16 ch 512 Hz 3 classes 4.0 s trials CC BY 4.0

Class Labels: both_feet, both_hands, rest

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Overview

CNBI EPFL Cybathlon BCI-race motor-imagery dataset

Dataset description

BCI training and competition data of the two tetraplegic pilots (MA25VE, AN14VE) of team Brain Tweakers (CNBI, EPFL) in the BCI race of the first Cybathlon (2016); 16 sensorimotor electrodes (g.USBamp, 512 Hz, GDF).

Only the offline calibration runs of the both-hands / both-feet / rest family are exposed. Runs are selected by their data-borne cue codes, not by file name (taskset names are spelled inconsistently, e.g. mi_bhbfrst vs mi_bhbfrest): a run is kept when its cues lie within {771, 773, 783} and include at least two of them. Runs with single-limb or tongue cues (e.g. mi_rlsf) and the incomplete / corrupted folders are skipped. Events are the class cues (after a ~3 s fixation, code 786), followed by ~4 s of feedback (781); the interval is 1-5 s after the cue. The GDF header only has generic eeg:<n> labels, so channels are renamed positionally, and the microvolt payload (unscaled by MNE) is converted to volts.

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Citation & Impact

Stimulus Protocol
../_images/Perdikis2018.svg

4s task window per trial · 3-class imagery paradigm · 1 runs/session across 1 sessions

HED Event Tags
HED tags3/3 events annotated

Source: MOABB BIDS HED annotation mapping.

Sensory-event
3
Label
2
Experimental-stimulus
1
Rest
1
Visual-presentation
1
rest
Sensory-eventExperimental-stimulusVisual-presentationRest
both_feet
Sensory-eventLabel
both_hands
Sensory-eventLabel

HED tree view

Tree · rest
├─ Sensory-event
├─ Experimental-stimulus
├─ Visual-presentation
└─ Rest
Tree · both_feet
├─ Sensory-event
└─ Label
Tree · both_hands
├─ Sensory-event
└─ Label
Channel Summary
Total channels16
EEG16 (Ag/AgCl)
Montage10-05
Sampling512 Hz
Notch / line50 Hz

This diagram is automatically generated from MOABB metadata. Please consult the original publication to confirm the experimental protocol details.

CNBI EPFL Cybathlon BCI-race motor-imagery dataset [1].

Dataset description

BCI training and competition data of the two tetraplegic pilots (MA25VE, AN14VE) of team Brain Tweakers (CNBI, EPFL) in the BCI race of the first Cybathlon (2016) [1]; 16 sensorimotor electrodes (g.USBamp, 512 Hz, GDF).

Only the offline calibration runs of the both-hands / both-feet / rest family are exposed. Runs are selected by their data-borne cue codes, not by file name (taskset names are spelled inconsistently, e.g. mi_bhbfrst vs mi_bhbfrest): a run is kept when its cues lie within {771, 773, 783} and include at least two of them. Runs with single-limb or tongue cues (e.g. mi_rlsf) and the incomplete / corrupted folders are skipped. Events are the class cues (after a ~3 s fixation, code 786), followed by ~4 s of feedback (781); the interval is 1-5 s after the cue. The GDF header only has generic eeg:<n> labels, so channels are renamed positionally, and the microvolt payload (unscaled by MNE) is converted to volts.

Warning

The online closed-loop and race recordings of the same archives are continuous-control (BrainRunners game) recordings and are intentionally not exposed by this loader, which serves only the cue-based offline calibration runs with discrete, data-borne class labels.

References

[1] (1,2)

Perdikis, S., Tonin, L., Saeedi, S., Schneider, C., & Millan, J. del R. (2018). The Cybathlon BCI race: Successful longitudinal mutual learning with two tetraplegic users. PLoS Biology, 16(5), e2003787. DOI: https://doi.org/10.1371/journal.pbio.2003787 Data: https://doi.org/10.5281/zenodo.841764

from moabb.datasets import Perdikis2018
dataset = Perdikis2018()
data = dataset.get_data(subjects=[1])
print(data[1])

Dataset summary

#Subj

2

#Chan

16

#Classes

3

Trials length

4 s

Freq

512 Hz

#Sessions

1

Participants

  • Population: spinal cord injury

  • Clinical population: tetraplegia (chronic spinal cord injury)

  • BCI experience: experienced

Equipment

  • Amplifier: g.USBamp (g.tec medical engineering, Austria)

  • Electrodes: Ag/AgCl

  • Montage: standard_1005

Preprocessing

  • Data state: raw

Data Access

Experimental Protocol

  • Paradigm: imagery

  • Feedback: visual

  • Stimulus: visual

Notes

Added in version 1.8.

__init__()[source]#

Initialize function for the BaseDataset.

property all_subjects#

Full list of subjects available in this dataset (unfiltered).

convert_to_bids(path=None, subjects=None, overwrite=False, format='EDF', verbose=None, generate_figures=False)[source]#

Convert the dataset to BIDS format.

Saves the raw EEG data in a BIDS-compliant directory structure. Unlike the caching mechanism (see CacheConfig), the files produced here do not contain a processing-pipeline hash (desc-<hash>) in their names, making the output a clean, shareable BIDS dataset.

Parameters:

  • path (str | Path | None) – Directory under which the BIDS dataset will be written. If None the default MNE data directory is used (same default as the rest of MOABB).

  • subjects (list of int | None) – Subject numbers to convert. If None, all subjects in subject_list are converted.

  • overwrite (bool) – If True, existing BIDS files for a subject are removed before saving. Default is False.

  • format (str) – The file format for the raw EEG data. Supported values are "EDF" (default), "BrainVision", and "EEGLAB".

  • verbose (str | None) – Verbosity level forwarded to MNE/MNE-BIDS.

  • generate_figures (bool) – If True, generate interactive neural signature HTML figures in {bids_root}/derivatives/neural_signatures/. Requires plotly (pip install moabb[interactive]). Default is False.

Returns:

bids_root – Path to the root of the written BIDS dataset.

Return type:

pathlib.Path

Examples

>>> from moabb.datasets import AlexMI
>>> dataset = AlexMI()
>>> bids_root = dataset.convert_to_bids(path="/tmp/bids", subjects=[1])

Notes

Use CacheConfig to configure caching for get_data(). Use moabb.datasets.bids_interface.get_bids_root to get the BIDS root path.

Added in version 1.5.

data_path(subject, path=None, force_update=False, update_path=None, verbose=None)[source]#

Download/extract the pilot’s archive; return [pilot_folder].

download(subject_list=None, path=None, force_update=False, update_path=None, accept=False, verbose=None)[source]#

Download all data from the dataset.

This function is only useful to download all the dataset at once.

When the dataset declares a nemar_id and the download provider is not "upstream", the files come from NEMAR’s sourcedata/ – the original pre-BIDS distribution, byte-identical to what the upstream host serves. On any NEMAR failure this falls back to the dataset’s own downloader with a warning (unless the provider is pinned to "nemar"). See sourcedata_path() and moabb.set_download_provider().

Parameters:

  • subject_list (list of int | None) – List of subjects id to download, if None all subjects are downloaded. On the NEMAR path each subject is resolved through the deposit’s sourcedata_provenance.json; deposits enriched before that manifest recorded subjects fetch the whole tree.

  • path (None | str) – Location of where to look for the data storing location. If None, the environment variable or config parameter MNE_DATASETS_(dataset)_PATH is used. If it doesn’t exist, the “~/mne_data” directory is used. If the dataset is not found under the given path, the data will be automatically downloaded to the specified folder.

  • force_update (bool) – Force update of the dataset even if a local copy exists.

  • update_path (bool | None) – If True, set the MNE_DATASETS_(dataset)_PATH in mne-python config to the given path. If None, the user is prompted. Not used on the NEMAR path.

  • accept (bool) – Accept licence term to download the data, if any. Default: False. Only relevant to the dataset’s own downloader; NEMAR mirrors are already public.

  • verbose (bool, str, int, or None) – If not None, override default verbose level (see mne.verbose()).

get_additional_metadata(subject: str, session: str, run: str)[source]#

Load additional metadata for a specific subject, session, and run.

This method is intended to be overridden by subclasses to provide additional metadata specific to the dataset. The metadata is typically loaded from an events.tsv file or similar data source.

Parameters:

  • subject (str) – The identifier for the subject.

  • session (str) – The identifier for the session.

  • run (str) – The identifier for the run.

Returns:

A DataFrame containing the additional metadata if available, otherwise None.

Return type:

None | pandas.DataFrame

get_block_repetition(paradigm, subjects, block_list, repetition_list)[source]#

Select data for all provided subjects, blocks and repetitions.

subject -> session -> run -> block -> repetition

See also

get_data

Parameters:

  • subjects (List of int) – List of subject number

  • block_list (List of int) – List of block number

  • repetition_list (List of int) – List of repetition number inside a block

Returns:

data – dict containing the raw data

Return type:

Dict

get_data(subjects=None, cache_config=None, process_pipeline=None, n_jobs=1)[source]#

Return the data corresponding to a list of subjects.

The returned data is a dictionary with the following structure:

data = {"subject_id": {"session_id": {"run_id": run}}}

subjects are on top, then we have sessions, then runs. A sessions is a recording done in a single day, without removing the EEG cap. A session is constitued of at least one run. A run is a single contiguous recording. Some dataset break session in multiple runs.

Processing steps can optionally be applied to the data using the *_pipeline arguments. These pipelines are applied in the following order: raw_pipeline -> epochs_pipeline -> array_pipeline. If a *_pipeline argument is None, the step will be skipped. Therefore, the array_pipeline may either receive a mne.io.Raw or a mne.Epochs object as input depending on whether epochs_pipeline is None or not.

Parameters:

  • subjects (List of int) – List of subject number

  • cache_config (dict | CacheConfig) – Configuration for caching of datasets. See CacheConfig for details.

  • process_pipeline (sklearn.pipeline.Pipeline | None) – Optional processing pipeline to apply to the data. To generate an adequate pipeline, we recommend using moabb.make_process_pipelines(). This pipeline will receive mne.io.BaseRaw objects. The steps names of this pipeline should be elements of StepType. According to their name, the steps should either return a mne.io.BaseRaw, a mne.Epochs, or a numpy.ndarray. This pipeline must be “fixed” because it will not be trained, i.e. no call to fit will be made.

  • n_jobs (int) – Number of jobs to run in parallel over subjects (passed to joblib.Parallel). Default 1 (sequential). Per-subject processing (reading, filtering, resampling, epoching) is independent, so this gives a near-linear speedup for datasets with many subjects.

Returns:

data – dict containing the raw data

Return type:

Dict

property metadata[source]#

Return structured metadata for this dataset.

Returns the DatasetMetadata object from the centralized catalog, or None if metadata is not available for this dataset.

Returns:

The metadata object containing acquisition parameters, participant demographics, experiment details, and documentation. Returns None if no metadata is registered for this dataset.

Return type:

DatasetMetadata | None

Examples

>>> from moabb.datasets import BNCI2014_001
>>> dataset = BNCI2014_001()
>>> dataset.metadata.participants.n_subjects
9
>>> dataset.metadata.acquisition.sampling_rate
250.0
sourcedata_path(subject=None, path=None, force_update=False, verbose=None)[source]#

Get the dataset’s original pre-BIDS distribution from NEMAR.

Where data_path() fetches the original files from the upstream host, this fetches the copy NEMAR mirrors under sourcedata/. The files keep their upstream names, so the two are interchangeable in content – but NEMAR stays reachable when the upstream host is slow, rate-limited, behind a bot gate, or retired.

Parameters:

  • subject (int | str | None) – Restrict the download to one subject, resolved through the deposit’s sourcedata_provenance.json. Deposits enriched before that manifest recorded subjects fall back to the whole tree with a warning. When None the whole tree is fetched.

  • path (None | str) – Base path where MOABB stores datasets.

  • force_update (bool) – Re-fetch even when a local copy is present.

  • verbose (bool, str, int, or None) – If not None, override default verbose level.

Returns:

Local path to the sourcedata directory.

Return type:

str

Raises:

  • ValueError – If the dataset declares no nemar_id.

  • moabb.datasets.download.NemarDownloadError – If the download fails or the deposit publishes no sourcedata/.