Overview
Summary: Perform preprocessing and quality assurance of 256 channel EEG data acquired with Netstation @ 250 Hz sample rate
Preprocessing Steps:
Import and re-reference to common average reference notch filter [58 62], low pass Butterworth filter [30Hz] order 4, high pass Butterworth filter [0.1Hz] order 1 Reject noisy channels based on spectral frequency [0.3 40 Hz] Perform EEGLAB FASTER ICA to remove artifact (muscle, eye blinks, eye movements); ICA components are rejected based on a z-score threshold of component properties (median gradient value, spectral slope around the LPF band,Hurst exponent, kurtosis of spatial map and eye blink correlations) Segment into trials based on trial definition (e.g. _Stroop) (default trials use 200ms baseline and 1000ms post-baseline) Apply automatic artifact rejection (default min rejection threshold -150 uV, default max rejection threshold 150 uV) Reinterpolate bad channels back into data
Quality Assurance Output:
Visualization of rejected ICA components Visualization of rejected channels displayed on 256 montage
Getting Started
The EEG egi256 preprocessing software runs inside a Singularity container. The container requires an "inputs" folder with the required inputs (i.e., eeg.raw, edat.txt files). The container also requires an "outputs" folder that will hold all the outputs after the pipeline runs. We also need to know the pre-trail baseline length (e.g. 200ms), the post-trail baseline length (e.g. 1000ms), which experimental condition was used when acquiring the data (i.e., either _Stroop, _Incidental, _Gonogo. With this information, we bind the inputs and outputs directories into the container to run the pipeline.
Containerization of Source Code
Command
singularity run --cleanenv --contain
--home $(pwd -P)/INPUTS
--bind INPUTS:/tmp
--bind INPUTS:/INPUTS
--bind OUTPUTS:/OUTPUTS
/path/to/EEG-EGI256-preproc_v1.0.0.simg
--out_dir /OUTPUTS
Input Directory:
.raw (eeg raw data)
.txt (netstation edat files converted to .txt)
Output Directory: Full outputs listed at the end of this document
The output preprocessed files are available in the PREPROCESSED subfolder in the output directory:
PREPROC_OUTPUT/eeg_ARTFREEDATA_${condition}.mat PREPROC_OUTPUT/eeg_badchannellist.mat PREPROC_OUTPUT/eeg_BadChannRemoved.mat PREPROC_OUTPUT/eeg_EOGCORR_trdat_${condition}.mat PREPROC_OUTPUT/eeg_goodchannellist.mat PREPROC_OUTPUT/eeg_GoodChannRemoved.mat PREPROC_OUTPUT/eeg_REFnFILT.mat PREPROC_OUTPUT/eeg_REPAIRED_AND_REFERENCED_${condition}.mat
The QA document is available in the QA subfolder in the output directory: