cmp.stages.eeg.esi module

Definition of config and stage classes for computing brain parcellation.

class cmp.stages.eeg.esi.EEGSourceImagingConfig[source]

Bases: traits.has_traits.HasTraits

Class used to store configuration parameters of a EEGSourceImagingStage instance.

task_label

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

Type

Str

esi_tool

Select the tool used for EEG source imaging (inverse solution)

Type

Enum

mne_apply_electrode_transform

If True, apply the transform specified below to electrode positions

Type

Bool

mne_electrode_transform_file

Instance of CustomEEGCartoolMNETransformBIDSFile that describes the input BIDS-formatted MNE transform file in fif format

Type

CustomEEGMNETransformBIDSFile

cartool_spi_file

Instance of CustomEEGCartoolSpiBIDSFile that describes the input BIDS-formatted EEG Solution Points Irregularly spaced file created by Cartool

Type

CustomEEGCartoolSpiBIDSFile

cartool_invsol_file

Instance of CustomEEGCartoolInvSolBIDSFile that describes the input BIDS-formatted EEG Inverse Solution file created by Cartool

Type

CustomEEGCartoolInvSolBIDSFile

cartool_esi_method

Cartool Source Imaging method

Type

Enum([‘LAURA’, ‘LORETA’])

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”])

cartool_esi_lamb

Regularization weight of inverse solutions computed with Cartool (Default: 6)

Type

Float

cartool_svd_toi_begin

Start TOI for SVD projection (Default: 0.0)

Type

Float

cartool_svd_toi_end

End TOI for SVD projection (Default: 0.25)

Type

Float

mne_esi_method

MNE Source Imaging method

Type

Enum([“sLORETA”, “eLORETA”, “MNE”, “dSPM”])

mne_esi_method_snr

SNR value such as the regularization weight lambda2 of MNE ESI method’ is set to 1.0 / mne_esi_method_snr ** 2 (Default: 3.0)

Type

Float

See also

cmp.stages.eeg.esi.EEGSourceImagingStage

class cmp.stages.eeg.esi.EEGSourceImagingStage(subject, session, bids_dir, output_dir)[source]

Bases: cmp.stages.common.Stage

Class that represents the reconstruction of the inverse solutions stage of a EEGPipeline.

If MNE is selected for ESI reconstruction, this stage consists of five processing interfaces:

  • CreateBem: Create the Boundary Element Model that consists of surfaces obtained with Freesurfer.

  • CreateSrc: Create a bilateral hemisphere surface-based source space file with subsampling.

  • CreateFwd: Create the forward solution (leadfield) from the BEM and the source space.

  • CreateCov: Create the noise covariance matrix from the data.

  • MNEInverseSolutionROI: Create and apply the actual inverse operator to generate the ROI time courses.

If you decide to use ESI reconstruction outputs precomputed with Cartool, then this stage consists of two processing interfaces:

  • CreateSpiRoisMapping: Create Cartool-reconstructed sources / parcellation ROI mapping file.

  • CartoolInverseSolutionROIExtraction: Use Pycartool to load inverse solutions estimated by Cartool and generate the ROI time courses.

See also

cmp.pipelines.functional.eeg.EEGPipeline, cmp.stages.eeg.esi.EEGSourceImagingConfig

create_cartool_workflow(flow, inputnode, outputnode)[source]

Create the stage workflow using Cartool-precomputed inverse solutions.

This method is called by create_workflow() main function if Cartool is selected for ESI.

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

create_mne_workflow(flow, inputnode, outputnode)[source]

Create the stage workflow using MNE.

This method is called by create_workflow() main function if MNE is selected for ESI.

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

create_workflow(flow, inputnode, outputnode)[source]

Main method to create the stage workflow.

Based on the tool used for ESI, this method calls either the create_cartool_workflow() or the :func:`~cmp.stages.eeg.esi.create_mne_workflow method.

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.