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B_STSW_ImportEyeEEG_180103
- Split EEG data into runs, combine EEG-ET data (eeglab toolbox)
C_STSW_prepare_preprocessing_180111
- Prepare for ICA
- Read into FieldTrip format
- Switch channels
- EEG settings:
o Referenced to avg. mastoid (A1, A2)
o downsample: 1000Hz to 250 Hz
o 4th order Butterworth 1-100 Hz BPF
o no reref for ECG
D_STSW_visual_inspection_for_ica_180105
- Check for gross noise periods that should not be considered for ICA
D2_STSW_carryOverVisualInspection
- If a previous step has to be redone, we want to carry over the indications about visually identified noise periods to the new config-structures
This had to be run as we needed to switch the channels (C_...) after originally keeping the original channel setup.
D3_correctMatrices_v2
- This script is a hack to deal with a previous script problem: During visual inspection, data may not have cleared from previous participants, thereby carrying over their labels of artifact periods. This script attempts to fix this problem by retaining only periods until the offset of the measured interval. A visual check indicated that this fixed the issue.
D5_InspectChannelArrangement
- Check whether the correlational structure of the channels looks sensible. If not, there may have been problems with electrode placement.
E_STSW_ica1_180108
- Conduct initial ICA1, this should be run on tardis
F_STSW_ICA_labeling_180111
- Manual labeling of artefactual ICA components
G_STSW_segmentation_raw_data_180111
- Segmentation: -1500 ms relative to fixcue onset to 1500 ms after ITI onset
- Load raw data
- Switch channels
- EEG settings:
o Referenced to avg. mastoid (A1, A2)
o 0.2 4th order butterworth HPF
o 125 4th order butterworth LPF
o demean
o recover implicit reference: A2
o downsample: 1000Hz 500 Hz
- Note that for Subject 1223 (runs 2,3,4) and 1228 (run 4), the script had to be fixed post-hoc as no ET data are available. The script …_noTardis was run on these repeat subjects. The same conditional has since been introduced into the main script, but it has not been recompiled.
- For subjects 2160 and 2203 the initial block onset triggers are missing. Dummy triggers are placed at the first events, but care should be taken in further preprocessing.
H_STSW_automatic_artifact_correction_20170922
- Automatic artifact correction, interpolation
- Remove blink, move, heart, ref, art & emg ICA components prior to calculation
- get artifact contaminated channels by kurtosis, low & high frequency artifacts
- get artifact contaminated channels by FASTER
- interpolate artifact contaminated channels
- equalize duration of trials to the trial with fewest samples
o This is a hack. Apparently, we did not always get consistent timing on each trial, such that some trials were a bit shorter. To include these trials, I cut every trial to the lowest trial length.
o Interpolation to a general length may be the better option.
- get artifact contaminated epochs & exclude epochs recursively
- get channel x epoch artifacts
- Note that this does NOT yet remove anything. We only calculate the data to be removed in the next setp (I).
I_STSW_prep_data_for_analysis_20170922
- Remove blink, move, heart, ref, art & emg ICA components
- Interpolate detected artifact channels
- Remove artifact-heavy trials, for subjects with missing onsets, the missing trials are included here as ‘artefactual trials’, hence correcting the EEG-behavior assignment:
Note that the channels A1 and FCz were generally exchanged in the BrainVisionRecorder. During some sessions, it was also apparent that the amplifiers had been switched. These channels have been switched based on visual inspection of the expected autocorrelation of neighboring channels (see C_figures/ C_ChannelCheck for the correlative structure afterwards). Note that this switching is only done AFTER the data are read into FieldTrip, i.e. the eeglab data have the WRONG channel assignment! The scripts that do the switching can be found in the directory A_scripts/helper/. C_STSW_prepare_preprocessing_180111 contains the conditionals for what is switched in which subject. Visual inspection of ICAs indicated that the channel switch was successful, although outlier channels may still be slightly off.