cmp.stages.connectome.eeg_connectome module

Definition of config and stage classes for building functional connectivity matrices from preprocessed EEG.

class cmp.stages.connectome.eeg_connectome.EEGConnectomeConfig[source]

Bases: traits.has_traits.HasTraits

Class used to store configuration parameters of a EEGConnectomeStage instance.

task_label

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

Type

Str

parcellation_scheme

Parcellation used to create the ROI source time-series

Type

Enum([“NativeFreesurfer”, “Lausanne2018”])

lausanne2018_parcellation_res

Resolution of the parcellation if Lausanne2018 parcellation scheme is used

Type

Enum([“scale1”, “scale2”, “scale3”, “scale4”, “scale5”])

connectivity_metrics

Set of frequency- and time-frequency-domain connectivity metrics to compute

Type

[‘coh’, ‘cohy’, ‘imcoh’, ‘plv’, ‘ciplv’, ‘ppc’, ‘pli’, ‘wpli’, ‘wpli2_debiased’]

output_types

Output connectome file format

Type

[‘tsv’, ‘gpickle’, ‘mat’, ‘graphml’]

class cmp.stages.connectome.eeg_connectome.EEGConnectomeStage(bids_dir, output_dir, subject, session='')[source]

Bases: cmp.stages.common.Stage

Class that represents the connectome building stage of a EEGPipeline.

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(log_visualization=True, circular_layout=False)[source]

Update the inspect_outputs class attribute.

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