erp pre-processing

DATA! NOW WHAT?Preparing your ERP data

for analysis

Dennis L. Molfese, Ph.D.

Caitlin M. Hudac, B.A.

Developmental Brain LabUniversity of Nebraska-Lincoln

1

Agenda

Pre-processing

Preparing for analysis steps

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EEG to ERP

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EEG to ERP

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EEG to ERP

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Pre-processing in NetStation

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ERP Pre-processingFilterFix high/low frequencies

SegmentationNeed to chop up EEG into ERP

Artifact detectionFix blinks, muscle movements, etc.

Artifact rejection

Bad channel correction

Channels with poor signal (e.g impedance, bad electrode)

AveragingRe-reference; combine trials

Baseline correction

ERP signal “level” may vary for each segment

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FilteringFiltering reduces total frequencies by specific amounts

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Filtering“60 cycle”: Without proper grounding, impedance between electrode and amplifier can become very large.

Causes: skin-to-skin contact, high-frequency interference from nearby electrical devices.

Adjust using a notch filter

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FILTERS CHANGE YOUR DATA!

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Filtering

Keep in mind:

Filters are additive -- the data changes each time you filter.

Use same filter settings (and amplifiers) for one dataset.

Try different filters out.

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Artifact rejection




Baseline correction


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Segmentation

Raw EEG signal “stamped” with stimulus event markers.

Segments are the length we want to choose for our ERP.

Can be different for each kind of stimulus.

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SegmentationEvent markers:

Codes are linked to objects in EPrime.

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Segmentation

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SegmentationOffsets:

Actual display of object will depend on the connection between PC (EPrime) and Mac (NetStation) computers.

PC sends stimulus

Stimulus presented

NetStation marks EEG

Time

Stimulus Offset

ba 6

da 4

ga 4

bu 5

du 7

gu 6

Offset

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Segmentation

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Segmentation

Visual InspectionEye channels could be poor due to no contact with skin or blinks/eye movements.

If poor across high number of trials, electrode must be marked “BAD” for entire recording.

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Artifact rejection




Baseline correction


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Artifact Strategy

First: Artifact Detection • Inspect Eye Channels• Check impedance levels from records• Have Artifact Detection check for you.Second: Artifact Rejection• Replace bad channels through spherical

interpolation

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What electrodes have bad or noisy signal?

Bad channels

Eye blinks

Eye movements

Define artifacts by threshold.

Ex: Max-Min = 200µV is bad channel over segment.

Define artifacts by slope of line -- how quickly does the signal change?

Define artifacts by modeling examples.

Artifact Detection

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Bad Channel Scan - shorted electrodes - bad scalp connection - 200 µV over segment

Eye Blinks & Movement -electrode pairs -differ by net type

Artifact Detection

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Eye Movements: 125 & 128

Eye Blinks:8 - 126, 26 - 127

Artifact Detection

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Be careful:

The algorithms can be too simple.

If eye channels detect an eye movement or blink, NetStation may mark the segment bad.

If an eye channel is bad, may mark all segments bad.

Artifact Detection

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Artifact Detection

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Artifact rejection




Baseline correction


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Artifact RegressionSpherical interpolation

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Artifact Regression• NetStation uses an “automatic ICA”

• Automatically removes eye movement and blink artifacts using blind component separation.

Prior to artifact regression

After artifact regression

(Joyce, Gorodnitsky, & Kutas, 2004)

with ocular artifacts

without ocular artifacts

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Artifact rejection




Baseline correction


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Baseline Correction• Important to avoid artifacts in baseline period!• Adjust pre-stimulus value (e.g. 100-200 ms) by

averaging across pre-stimulus points during baseline. • Subtract average value from post-stimulus period.

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Artifact rejection




Baseline correction


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Bad Channel Correction

No user settings. Instead, we interpolate missing channels using weighted average.

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Artifact rejection




Baseline correction


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Average Reference

Why re-reference? Data originally recorded to represent the difference between an electrode and reference (Cz).

Define a new “zero point”.

Using an average reference reduces the bias of a particular reference.

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Average Reference

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Averaging trials•Averaging is a noise reduction technique.•Combine trials to form a single averaged waveform.

What trials to average?• same condition (happy faces)• all stimulus of one type (happy,

angry, and fearful faces)

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Important Strategies to keep in mind:

Equal Number of Averages / Condition

Equal Number of Averages / Subject

Weighted Averaging

Random Selection of Trials

Early vs. Late in Experiment

Averaging

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Automating analyses

Build scripts for each study.

Easy -- just drag and drop!

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Controversy of Order

Does the order of operation change the data?

• Baseline Correction • Re-referencing the data• Averaging segments

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1. Average2. Average reference3. Baseline correction

1. Average reference Average2. Baseline correction

1. Baseline correction Average2. Average reference

Controversy of Order

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Pre-processed data: Now what?

Perform NetStation analyses

Peak amplitude /latency

Export data to work in statistical package of choice (e.g. SPSS, SAS, MATLAB).

Rotate the data?

Combine regional electrodes?

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Exporting data

Use NetStation exporter (AVG --> RAW) then convert using Text Exporter program (RAW --> TXT)

Use File Export tool in Netstation

!

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Exporting dataBE CAREFUL ABOUT FILE NAMING!

One text file per person per condition

00001_6x25.ave_ba.txt00001_6x25.ave_da.txt00001_6x25.ave_ga.txt00001_6x25.ave_bu.txt00001_6x25.ave_du.txt00001_6x25.ave_gu.txt00001_6x25.ave.RAW00002_6x25.ave_ba.txt00002_6x25.ave_da.txt00002_6x25.ave_ga.txt00002_6x25.ave_bu.txt00002_6x25.ave_du.txt00002_6x25.ave_gu.txt00002_6x25.ave.RAW

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1. Rotate data matrix for input to stat programs.2. Concatenate subject data text files.3. Combine electrode sites into regional electrodes.

MCAT Program

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BEFORE AFTER

Suitable for Temporal PCASuitable for Spatial PCA

MCAT Program1. Rotate data matrix for input to stat programs.2. Concatenate subject data text files.3. Combine electrode sites into regional electrodes.

Channel 1Data Pt 1

Channel 2Data Pt 1

Channel 3Data Pt 1

Channel 1Data Pt 2

Channel 2Data Pt 2

Channel 3Data Pt 2

Channel 1Data Pt 3

Channel 2Data Pt 3

Channel 3Data Pt 3

Channel 1Data Pt 1

Channel 2Data Pt 1

Channel 3Data Pt 1

Channel 1Data Pt 2

Channel 2Data Pt 2

Channel 3Data Pt 2

Channel 1Data Pt 3

Channel 2Data Pt 3

Channel 3Data Pt 3

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00001_6x25.ave_ba.txt

00001_6x25.ave_da.txt

00001_6x25.ave_ga.txt

00001_6x25.ave_bu.txt

00001_6x25.ave_du.txt

00001_6x25.ave_gu.txt

00001_6x25.ave.RAW

00001_6x25.ave_ba.txt +00001_6x25.ave_da.txt +00001_6x25.ave_ga.txt +00001_6x25.ave_bu.txt +00001_6x25.ave_du.txt +00001_6x25.ave_gu.txt

00001_6x25.ave.RAW

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REF

CZ

101

Pz

COM

15387

36 224

59

C3

183

C4

21

37 18

47

F7

2

F8

116 150

17096

202

T4

69

T3

13

4

5

6

7

8

9

1011

12

13

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Fz

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Fp2

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Fp1

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F3

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7172

186

198

207

215

74

7576 77

7879

80

81

73

253

252

248

249

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255

256

251

250

241

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242

245

243

246

247

82

83

8485

86

P3

88

89

90

91

92

9394

LM95

T5 9798

99

100

102

103

104105

106 107108

109

110

111

112

113 114115

117

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120 121 122123

124

O1

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133134

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Oz

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O2

151

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P4

163

164173

165

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S/N

174

167

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132144

175

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T6

179

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RM

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194184185

195196

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F4

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238 239240

HydroCel Geodesic Sensor Net

256 Channel MapVersion 1.0

For questions or additional assistance please refer to the EGI Sensor Net Technical Manual or contact us at:

Electrical Geodesics, Inc.

1600 Millrace Drive, Suite 307

Eugene, Oregon 97403

Phone: (541) 687-7962 Fax:(541) 687-7963

Email: [email protected] or [email protected]


REF

CZ

101

Pz

COM

15387

36 224

59

C3

183

C4

21

37 18

47

F7

2

F8

116 150

17096

202

T4

69

T3

13

4

5

6

7

8

9

1011

12

13

14

15

Fz

16

17

19

Fp2

20

22

23

24

25

26

27

28

29

30

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Fp1

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35

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F3

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54

55

56

57

58

60

61

62

63

64

65

66

67

68

70

7172

186

198

207

215

74

7576 77

7879

80

81

73

253

252

248

249

254

255

256

251

250

241

244

242

245

243

246

247

82

83

8485

86

P3

88

89

90

91

92

9394

LM95

T5 9798

99

100

102

103

104105

106 107108

109

110

111

112

113 114115

117

118

119

120 121 122123

124

O1

125

126

127

128

129

130

131

133134

135

136

137

Oz

138

139

140

141

142

143

145

146

147

148

149

O2

151

152

154

155

156

157

158

159

160

161

162

P4

163

164173

165

166

S/N

174

167

168

169

171

172

132144

175

176

177

178

T6

179

180

181

182

187

188

189

190

RM

191

192

193

194184185

195196

197

199

200

201

210

208

209

216

217

218

203

204205

206

214

F4

211

212213 219

220

221222

223 225

226

227

228

229

230

231

232

233

234235

236

237

238 239240







Phone: (541) 687-7962 Fax:(541) 687-7963


256 Hydrocel Net50

MCAT Program

REF

CZ

101

Pz

COM

15387

36 224

59

C3

183

C4

21

37 18

47

F7

2

F8

116 150

17096

202

T4

69

T3

13

4

5

6

7

8

9

1011

12

13

14

15

Fz

16

17

19

Fp2

20

22

23

24

25

26

27

28

29

30

31

32

33

Fp1

34

35

38

39

40

41

F3

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48

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50

51

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53

54

55

56

57

58

60

61

62

63

64

65

66

67

68

70

7172

186

198

207

215

74

7576 77

7879

80

81

73

253

252

248

249

254

255

256

251

250

241

244

242

245

243

246

247

82

83

8485

86

P3

88

89

90

91

92

9394

LM95

T5 9798

99

100

102

103

104105

106 107108

109

110

111

112

113 114115

117

118

119

120 121 122123

124

O1

125

126

127

128

129

130

131

133134

135

136

137

Oz

138

139

140

141

142

143

145

146

147

148

149

O2

151

152

154

155

156

157

158

159

160

161

162

P4

163

164173

165

166

S/N

174

167

168

169

171

172

132144

175

176

177

178

T6

179

180

181

182

187

188

189

190

RM

191

192

193

194184185

195196

197

199

200

201

210

208

209

216

217

218

203

204205

206

214

F4

211

212213 219

220

221222

223 225

226

227

228

229

230

231

232

233

234235

236

237

238 239240







Phone: (541) 687-7962 Fax:(541) 687-7963


256 Hydrocel Net

1. Rotate data matrix for input to stat programs.2. Concatenate subject data text files.3. Combine electrode sites into regional electrodes.

51

!

For Temporal PCA analyses, “drag ‘n drop” text files.

MCAT Program

52

!

MCAT Program

Subject 00001

Time points for “ba”

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Summary

Pre-processing involves making informed decisions about your data!

Review the literature for similar paradigms to decide how to start.

Make a plan -- be prepared and organized.

It’s okay to revise your plan!

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QUESTIONS ???

[email protected]@huskers.unl.edu

[email protected]

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MCAT

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MCAT to SPSS

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erp pre-processing

Documents