cmp.stages.eeg.preprocessing module

Definition of config and stage classes for computing brain parcellation.

class cmp.stages.eeg.preprocessing.EEGPreprocessingConfig[source]

Bases: traits.has_traits.HasTraits

Class used to store configuration parameters of a EEGPreprocessingStage instance.

task_label

Task label (e.g. _task-<label>_)

Type

Str

eeg_ts_file

Instance of CustomEEGPreprocBIDSFile that describes the input BIDS-formatted preprocessed EEG file

Type

CustomEEGPreprocBIDSFile

events_file

Instance of CustomEEGEventsBIDSFile that describes the input BIDS-formatted EEG events file

Type

CustomEEGEventsBIDSFile

electrodes_file_fmt

Select the type of tabular file describing electrode positions

Type

Enum([“BIDS”, “Cartool”])

bids_electrodes_file

Instance of CustomEEGElectrodesBIDSFile that describes the input BIDS-compliant EEG electrode file

Type

CustomEEGElectrodesBIDSFile

cartool_electrodes_file

Instance of CustomEEGCartoolElectrodesBIDSFile that describes the input BIDS-formatted EEG electrode file created by Cartool

Type

CustomEEGCartoolElectrodesBIDSFile

t_min

Start time of the epochs in seconds, relative to the time-locked event (Default: -0.2)

Type

Float

t_max

End time of the epochs in seconds, relative to the time-locked event (Default: 0.5)

Type

Float

See also

cmp.stages.eeg.preparer.EEGPreprocessingStage

class cmp.stages.eeg.preprocessing.EEGPreprocessingStage(subject, session, bids_dir, output_dir)[source]

Bases: cmp.stages.common.Stage

Class that represents the preprocessing stage of a EEGPipeline.

This stage consists of converting EEGLab set EEG files to MNE Epochs in fif format, the format used in the rest of the pipeline by calling, if necessary the following interface:

  • EEGLAB2fif: Reads eeglab data and converts them to MNE format (fif file extension).

See also

cmp.pipelines.functional.eeg.EEGPipeline, cmp.stages.eeg.preparer.EEGPreprocessingConfig

create_workflow(flow, inputnode, outputnode)[source]

Create the stage workflow.

Parameters

  • flow (nipype.pipeline.engine.Workflow) – The nipype.pipeline.engine.Workflow instance of the EEG pipeline

  • inputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the inputs of the stage

  • outputnode (nipype.interfaces.utility.IdentityInterface) – Identity interface describing the outputs of the stage

define_inspect_outputs()[source]

Update the inspect_outputs class attribute.

It contains a dictionary of stage outputs with corresponding commands for visual inspection.