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Stimic - Analysis - Artefact evolution across contacts

jeu. 08 novembre 2018 by Martin Deudon

Download the notebook : stimic_artefact_distance.py

Shape evolution of the stimulation artefact along the electrode

In this notebook, we analyse how the shape of the artefact changes when the distrance from the recording site to the stimulation site increases.

In [3]:
%matplotlib inline
import matplotlib
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import mne
from stim_analysis_fun import *
sns.set_context('paper')
sns.set()
import re

Set the path of the epoch and stim event list :

In [4]:
stim_epoch_path = r'C:\\Users\\deudon\\Desktop\\Stimic\\_Data\\STIMS\\P53_CD25\\P53_CD25_stim_mne_epoch-resync-epo.fif'
stim_spreadsheet_path = r'C:\Users\deudon\Desktop\Stimic\_Data\STIMS\P53_CD25\p53_CD25_stimulations_all.xlsx'

Read mne epoch structure :

In [5]:
stim_epoch = mne.read_epochs(stim_epoch_path)
print(stim_epoch)

Reading C:\\Users\\deudon\\Desktop\\Stimic\\_Data\\STIMS\\P53_CD25\\P53_CD25_stim_mne_epoch-resync-epo.fif ...
Isotrak not found
    Found the data of interest:
        t =   -5000.00 ...   24998.05 ms
        0 CTF compensation matrices available
182 matching events found
182 matching events found
0 projection items activated
<EpochsFIF  |  n_events : 182 (all good), tmin : -5.0 (s), tmax : 24.998046875 (s), baseline : None, ~2.44 GB, data loaded>

Load stim spreadsheet :

In [6]:
df = pd.read_excel(stim_spreadsheet_path)

Let's call the plot_artefact_ev_with_electrode_distance function.

The two arguments are respectively the MNE epoch structure containing the stimulation data and the pandas DataFrame listing all the stimulations. The 3rd argument is the channel maximal offset, i.e. how far from the stimulation site we look at the shape of the stimulation artefact.

The function can be called with optionnal selection arguments which must be column names of the stimulation data frame df. For instance :

  • plot_artefact_ev_with_electrode_distance(stim_epoch, df, 1, freq=1) will select only the 1Hz stimulations
  • plot_artefact_ev_with_electrode_distance(stim_epoch, df, 1, freq=1, intensity=1.5) will select only the 1Hz stimulations at 1.5 mA intensity
  • plot_artefact_ev_with_electrode_distance(stim_epoch, df, 1, freq=50, channelname='EEG A3') will select the 50Hz stimulation located in EEG A3
In [7]:
plot_artefact_ev_with_electrode_distance(stim_epoch, df, 1, freq=50)