cmp.pipelines.functional.eeg module

EEG pipeline Class definition.

class cmp.pipelines.functional.eeg.EEGPipeline(project_info)[source]

Bases: cmp.pipelines.common.Pipeline

Class that extends a Pipeline and represents the processing pipeline for EEG.

It is composed of:

the EEG preprocessing stage that loads the input preprocessed EGG Epochs files and convert them to the MNE fif format.
the EEG source imaging stage that takes care of all the steps necessary to extract the ROI time courses.
the EEG connectome stage that computes different frequency- and time-frequency-domain connectivity measures from the extracted ROI time courses.

check_config()[source]

check_input()[source]

Check if input of the eeg pipeline are available (Not available yet).

Returns: valid_inputs – True if inputs are available
Return type: bool

create_datagrabber_node(name='eeg_datasource', base_directory=None, debug=False)[source]

Create the appropriate Nipype BIDSDataGrabber node depending on the configuration of the different EEG pipeline stages.

Parameters

name (str) – Name of the datagrabber node
base_directory (str) – Path to the directory that store the check_input node output
debug (bool) – Print extra debugging messages if True

Returns

datasource – Output Nipype Node with BIDSDataGrabber interface

Return type

Output Nipype BIDSDataGrabber Node

create_datasinker_node(output_directory)[source]

Create the appropriate Nipype DataSink node depending on EEG task_label and parcellation_scheme

Parameters: output_directory (Directory) – Main CMP output directory of a subject e.g. /output_dir/cmp/sub-XX/(ses-YY)
Returns: sinker – Output Nipype Node with DataSink interface
Return type: Output Nipype DataSink Node

create_pipeline_flow(cmp_deriv_subject_directory, nipype_deriv_subject_directory)[source]

Create the workflow of the EEG pipeline.

Parameters

cmp_deriv_subject_directory (Directory) – Main CMP output directory of a subject e.g. /output_dir/cmp/sub-XX/(ses-YY)
nipype_deriv_subject_directory (Directory) – Intermediate Nipype output directory of a subject e.g. /output_dir/nipype/sub-XX/(ses-YY)

Returns

eeg_flow – An instance of nipype.pipeline.engine.Workflow

Return type

nipype.pipeline.engine.Workflow

get_nipype_eeg_pipeline_subject_dir()[source]: Return the path to Nipype eeg_pipeline folder of a given subject / session.

global_conf = <cmp.pipelines.functional.eeg.GlobalConfig object>

init_subject_derivatives_dirs()[source]

Return the paths to Nipype and CMP derivatives folders of a given subject / session.

Notes

self.subject is updated to “sub-<participant_label>_ses-<session_label>” when subject has multiple sessions.

input_folders = ['anat', 'eeg']

now = '20240815_1553'

ordered_stage_list = ['EEGPreparer', 'EEGLoader', 'InverseSolution']

process()[source]: Executes the anatomical pipeline workflow and returns True if successful.

class cmp.pipelines.functional.eeg.GlobalConfig[source]

Bases: traits.has_traits.HasTraits

Global EEG pipeline configurations.

process_type

Processing pipeline type

Type: ‘EEG’

subjects

List of subjects ID (in the form sub-XX)

Type: traits.List

subject

Subject to be processed (in the form sub-XX)

Type: traits.Str

subject_session

Subject session to be processed (in the form ses-YY)

Type: traits.Str