neuralset.extractors.neuro.IeegExtractor

class neuralset.extractors.neuro.IeegExtractor(*, event_types: Literal['Ieeg'] = 'Ieeg', aggregation: Literal['single', 'sum', 'mean', 'first', 'middle', 'last', 'cat', 'stack', 'trigger'] = 'single', allow_missing: bool = False, frequency: Literal['native'] | float = 'native', offset: float = 0.0, baseline: tuple[float, float] | None = None, picks: Annotated[tuple[str, ...], MinLen(min_length=1)] = ('seeg', 'ecog'), apply_proj: bool = False, filter: tuple[float | None, float | None] | None = None, apply_hilbert: bool = False, notch_filter: float | list[float] | None = None, drop_bads: bool = False, mne_cpus: int = -1, infra: MapInfra = MapInfra(folder=None, cluster=None, logs='{folder}/logs/{user}/%j', job_name=None, timeout_min=120, nodes=1, tasks_per_node=1, cpus_per_task=10, gpus_per_node=None, mem_gb=None, max_pickle_size_gb=None, slurm_constraint=None, slurm_partition=None, slurm_account=None, slurm_qos=None, slurm_use_srun=False, slurm_additional_parameters=None, conda_env=None, workdir=None, permissions=511, version='1', keep_in_ram=True, max_jobs=128, min_samples_per_job=1, forbid_single_item_computation=False, mode='cached'), scaler: None | Literal['RobustScaler', 'StandardScaler'] = None, scale_factor: float | None = None, clamp: float | None = None, fill_non_finite: float | None = None, bipolar_ref: tuple[list[str], list[str]] | None = None, channel_order: Literal['unique', 'original'] = 'unique', allow_maxshield: bool = False, reference: Literal['bipolar'] | None = None)[source][source]

Intracranial EEG feature extractor.

Parameters:

  • picks (default = ("seeg", "ecog", )) – pick “seeg” and “ecog” channels by default.

  • reference ("bipolar" or None, default=None) – If “bipolar”, applies a bipolar reference to the data, i.e., uses neighboring electrode as reference. Uses mne.set_bipolar_reference under the hood. [ieeg1]

Notes

Bipolar reference currently can only be applied to sEEG. It expects that the channels in raw.ch_names are ordered by probe, and with ascending order for each probe, and the names consists of the probe name followed by the position on the probe. eg: [‘OF1’, ‘OF2’, ‘OF3’, … , ‘OF12’, ‘OF13’, ‘OF14’, ‘H1’, ‘H2’, ‘H3’, … , ‘H13’, ‘H14’, ‘H15’, …]

WATCH-OUT: this will take the closest electrode on the probe, meaning that if the neighboring electrode is missing for some reason (eg: rejected before applying the reference) then the next electrode will be used for referencing.

References