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36 protocols using eeglab toolbox

1

EEG Preprocessing for Motor Cortex Analysis

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All offline analyses were performed using the EEGLAB toolbox (Delorme and Makeig, 2004 (link)) and Matlab2015b (The MathWorks Inc. Natick, MA, USA). The data was processed in General Data Format (GDF). Considering the large number of electrodes used in this study (e.g., =128) and the purpose of this research (motor patterns over the motor cortex) we chose to use a common average referencing (CAR) performed using EEGLAB (Dien, 1998 ; Lei and Liao, 2017 (link)). The results were also visualized by applying a Laplacian filter and a Mastoidal re-referencing and confirmed those described below (Perrin et al., 1989 (link)). Then, EEG signals were resampled at 128 Hz and divided into 9 s epochs corresponding to 2 s before and 7 s after the motor task for each run. Finally, we removed the trials containing muscle artifacts that may have affected ERD/ERS modulations. For this purpose, we used the EMG electrode present throughout the experiment. We also eliminated trials which included ERDs and ERS outlayers (i.e., ERDs and ERSs that significantly exceeded the confidence interval for the same run). The number of trials deleted are described in the corresponding result section (see section 3.1).
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2

Auditory ERP Processing and Analysis

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Electrophysiological signals were further processed off-line using Curry 7 software (Compumedics). Recordings were first down-sampled to 250 Hz. Data were then re-referenced to a common average reference and filtered using a bandpass frequency of 0.3–30 Hz. All EEG and EOG recordings were visually inspected to reject gross artifacts, such as those involving movement. Eye blinks and eye movements were corrected based on the artifact reduction method developed by Semlitsch et al.49 (link). Data were segmented into 1,000-msec epochs, which included the 100 msec prior to stimulus onset. All segments with voltage > ±70 µV were automatically discarded from further processing. Trials with response times >800 msec were considered error responses and were rejected. Only those trials with correct responses at the five midline sites (Fz, FCz, Cz, CPz, and Pz) to the infrequent stimuli were averaged and analyzed. The ERP waveforms of each participant had a minimum of 30 artifact-free trials. The auditory P300 was identified as the most positive peak in a 248–500-msec time window following stimulus onset. The auditory N100 component was defined as the most negative peak in the latency range of 80–180 msec. Topographic maps were created using Matlab 7.10.0 (MathWorks, Natick, MA, USA) and EEGLAB toolbox50 (link).
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3

EEG Functional Connectivity Analysis

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The measurements of the electrical brain activity were analyzed by means of the same EEGLAB-toolbox as mentioned in EEG Data Preprocessing (MathWorks, United States; Swartz Center of Computational Neuroscience, San Diego, CA, United States) (Delorme and Makeig, 2004 (link)). Functional connectivity analyses COH and ICOH were conducted by means of the Matlab-based METH-toolbox (MEG and EEG Toolbox of Hamburg) (Dept. of Neurophysiology and Pathophysiology; University Medical Center Hamburg-Eppendorf).
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4

Electrophysiological Signatures in Stroop Task Performance

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While participants performed the Stroop task, EEG data were recorded from 32 Ag/AgCl scalp electrodes (BrainCap, GmbH, Germany) according to the international 10–20 system. The placement of the recording reference was at Cz, while the ground was positioned at approximately AFz. The impedances were kept below 10 kΩ with the sampling frequency at 1,000 Hz.
Utilizing MATLAB (MathWorks, Natick, MA, United States) and the EEGLAB toolbox (Delorme and Makeig, 2004 ), we processed the continuous EEG data with in-house scripts. An offline digital band-pass filter (0.1–30 Hz) was applied. Epochs were extracted from −200 to 1,000 ms relative to the onset of the word stimulus and baseline corrected using the prestimulus interval (−200 to 0 ms). Independent component analysis (ICA) was used to correct eye movement, muscle artifacts, and heartbeat artifacts. All EEG epochs were processed for artifact detection by visual inspection and EEGLAB, and detection of obvious eye blinks and epochs with amplitude values exceeding ±100 mV at any electrode were rejected and later re-referenced to the average reference (Tafuro et al., 2019 (link); Overbye et al., 2021 (link)). To guarantee the quality of data, patients with >20% of bad epochs for each condition and/or five bad channels were removed from the analysis, and one MAP- participant with more than 20% of bad epochs was excluded.
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5

Connectivity Analysis of Neurophysiological Data

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The significant difference between the degree centralities at the nodes for KMI and VMI was calculated for each frequency band using a non-parametric permutation test. The significance was evaluated by the permutation distribution with 10,000 iterations40 (link). Pearson's correlation coefficient (R) was calculated to measure the similarity between the connectivity matrixes of the different conditions. All analyses were conducted with MATLAB (R2018a, Math-Works, Natick, MA, USA) and the EEGLAB toolbox41 (link).
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6

EEG Acquisition and Microstate Analysis

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An actiCHamp amplifier (Brain Vision LLC, NC, United States) was used to amplify and digitize the EEG data at a sampling frequency of 512 Hz. The EEG data were stored in a PC running Windows 7 (Microsoft Corporation, Washington, DC, United States). EEG activity was recorded from 64 positions with active Ag/AgCl scalp electrodes (actiCAP electrodes, Brain Vision LLC, NC, United States). The ground and reference electrodes were placed on AFz and on FCz, respectively (see Figure 1).
Electroencephalography acquisition was carried out by NeuroRT Studio software (Mensia Technologies SA, Paris, France). The EEG signal processing procedure was performed using MATLAB functions (MathWorks Inc., Natick MA, United States), specifically the EEGLab toolbox (Delorme and Makeig, 2004 (link)). EEG microstates were extracted and characterized by LORETA-KEY v20170220 software (the Key Institute for Brain-Mind Research, Zurich, Switzerland). Statistical analyses were performed by SPSS for Windows, version 23.0 (IBM Inc., Chicago, IL, United States).
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7

EEG Preprocessing for Cognitive Experiments

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EEG data were acquired by an amplifier (actiCHamp, Brain Products GmBH, Gilching, Germany) with 32-channel wet electrodes, with a sampling rate of 500 Hz. Ground and reference electrodes were attached at the left and right mastoid, respectively. EEG data were preprocessed through a pipeline set in the following order: high-pass filtering (>0.5 Hz), bad channel rejection, common average re-referencing, low-pass filtering (<50 Hz), and artifact subspace reconstruction (ASR). EEG data were epoched from −200 to 600 ms after stimulus onset, and baseline correction was conducted with baseline data from −200 ms to onset. After epoching, EEG data were standardized by removing the mean and scaling to unit variance. For preprocessing, EEGLAB Toolbox [20 (link)], MATLAB (The MathWorks, Inc., Natick, MA, USA), and Python (Python Software Foundation, Beaverton, OR, USA) were used together.
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8

EEG Data Analysis with EEGLAB and Matlab

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EEG data were analysed via custom routines based on EEGLAB toolbox [36 (link)] and Matlab R2017b (MathWorks, Natick, MA, USA). Continuous EEG signals were band-pass filtered between 7 and 25 Hz (with the exclusion of the sigma frequency band by notch filter centered on 13 Hz with a bandwidth at 4 Hz) and between 0.3 and 4.5 Hz, in order to identify the fast and the slow components of the CAP A phases, respectively [29 (link)].
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9

EEG Protocol for Visual Perception

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Electroencephalographic data were recorded from a 64-electrode scalp cap using the 10–20 system (Brain Products, Munich, Germany) with reference electrodes on the left and right mastoids. The vertical electrooculogram (EOG) was recorded with placed above and below the left eye. EEG and EOG activity was amplified at 0.01–100 Hz band-pass and sampled at 500 Hz. All of the electrode impedances were maintained below 5 kΩ.
The EEG data were pre-processed and analyzed using Matlab R2011b software (MathWorks) and the EEGLAB toolbox (Delorme and Makeig, 2004 (link)). The EEG data for each electrode were down-sampled to 250 Hz and re-referenced to the grand averages. The signal was then passed through a 0.01- to 30-Hz band-pass filter. Time windows of 200 ms before and 700 ms after the onset of the picture were segmented. EOG artifacts were corrected using an independent component analysis (ICA) (Jung et al., 2001 (link)) (Supplementary Figure S1). Epochs with amplitudes that exceeded ±50 μV at any electrode were excluded from the average (5.6 ± 0.6% trials were excluded).
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10

EEG Acquisition and Preprocessing for Epilepsy

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Each participant could perform routine long-term EEG recording. We used the Nicolet EEG machine to record the EEG at a sampling rate of 500 Hz. The scalp electrodes were placed under the international 10–20 montage system, and the A1 and A2 electrodes were used as references. EEG was performed in the same recording room using the same system, and the same EEG technician used conventional measurement techniques to determine the electrodeposition. We collected EEG for at least 15 h with the subjects relaxed, asleep, and their eyes closed to avoid disturbance. All EEG records contained 19 scalp electrodes (Fp1, Fp2, F7, F3, Fz, F4, F8, T3, C3, Cz, C4, T4, T5, P3, Pz, P4, T6, O1, and O2) and a visual inspection by EEG technician was performed.
We extracted the ictal phase data from raw EEG of PE group under the guidance of professional neurology clinicians; as a result, we had only various ictal phases linked together of each PE participant in the EEG data. To reduce data volume and speed up computation, we down-sampled the data to 100 Hz. Then, the data was filtered with band-pass at frequencies of 0.5 and 45 Hz. Finally, automated artifact removal was performed on the manually processed dataset using the independent components algorithm (ICA). These preprocessing steps were operated using EEGLab toolbox [18 (link)] in MATLAB (MathWorks).
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