ephypype.pipelines.create_pipeline_source_reconstruction

ephypype.pipelines.create_pipeline_source_reconstruction(main_path, subjects_dir, pipeline_name='inv_sol_pipeline', spacing='ico-5', inv_method='MNE', snr=1.0, is_epoched=False, events_id={}, condition=None, decim=1, t_min=None, t_max=None, is_evoked=False, parc='aparc', aseg=False, aseg_labels=[], noise_cov_fname='', all_src_space=False, ROIs_mean=True, save_mixed_src_space=False, is_fixed=False)

Source reconstruction pipeline.

Parameters:

main_pathstr

the main path of the workflow

subjects_dirstr

Freesurfer directory

pipeline_namestr (default inv_sol_pipeline)

name of the pipeline

spacingstr (default ‘ico-5’)

spacing to use to setup a source space

inv_methodstr (default MNE)

the inverse method to use; possible choices: MNE, dSPM, sLORETA

is_epochedbool (default False)

if True and events_id = None the input data are epoch data in the format -epo.fif if True and events_id is not None, the raw data are epoched according to events_id and t_min and t_max values

is_fixedbool (default False)

if True we use fixed orientation, otherwise the loose orientation is applied

events_id: dict (default None)

the dict of events

t_min, t_max: int (defualt None)

define the time interval in which to epoch the raw data

is_evoked: bool (default False)

if True the raw data will be averaged according to the events contained in the dict events_id

parc: str (default ‘aparc’)

the parcellation defining the ROIs atlas in the source space

aseg: bool (defualt False)

if True a mixed source space will be created and the sub cortical regions defined in aseg_labels will be added to the source space

aseg_labels: list (default [])

list of substructures we want to include in the mixed source space

noise_cov_fname: str (default None)

template for the path to either the noise covariance matrix file or the empty room data

all_src_space: bool

if True we compute the inverse for all points of the source space

ROIs_mean: bool

if True we compute the mean of estimated time series on ROIs

save_mixed_src_space: bool (defualt False)

if True the mixed src space will be saved in the FS folder

raw (inputnode): str

path to raw data in fif format

sbj_id (inputnode): str

subject id

trans_file (inputnode): str

path to coregistration file

events_file (inputnode): str

path to events file if is_evoked = True

Returns:

pipelineinstance of Workflow