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PSY250
Datacollection/handling: Dataanalysisandinterpretation
Dr.Haline Schendan
Officehours:w1011,Fr 1112,PSQA208
Outline
Meeting1:Introductiontotheelectroencephalogram (EEG).RawEEGandartifactdetection.Sortingdata intoconditions. Meeting2:Introductiontoeventrelatedpotentials (ERPs).Averaging,filtering,measuring,displaying. Meeting3:StatisticalanalysisofERPs.Individualvs. Groupresults. Meeting4:Interpretation of(EEGand)ERPresults. Writingamethodssection,aresultssection,anda summarysectionofthediscussion.Interpreting results,makingconclusions,avoidingcommon interpretationalflaws.
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Assessment
Pass/failsubcomponent+100%graded8page experimentproposal(with10%deductedif subcomponentfailed). Pass/Fail:preprocessingofarawdataset, includinggeneratingasetofartifactrejection thresholds(Meeting1homework);includingprintout ofERPplots(Meeting2homework);statistical analysisofthepreprocesseddata,includingSPSS printout(Meeting3homework). 100%graded:8pageessayproposingonenovel ERPexperiment.
Assessment
Experimentproposalessaymustinclude:
Clearrationale forthestudy,includingwhichERP componentswillbeaffectedandhow,andatwhattimethe effectswillbe observed Detailedmethods section,includingdatarecording,pre processing,andstatisticalanalysis Predicted results sectionandconclusion EssaymustdemonstratebasicknowledgeofEEG/ERP methodsfromreadinglistandmustincluderelevant citationsandreferencestopriorERPexperiments Topic
Perceptionorcognitionofobjects,faces,orscenes Memory
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Reading List
Luck,S.J.(2005).Anintroductiontotheeventrelated potentialtechnique.Cambridge,MA:MITPress.(10 copiesinlibrary) Picton,T.W.,Bentin,S.,Berg,P.,Donchin,E.,Hillyard, S.A.,Johnson,R.,Jr.,&Taylor,M.J.(2000).Guidelines forusinghumaneventrelatedpotentialstostudy cognition:recordingstandardsandpublication criteria.Psychophysiology,37(2),127152. Woodman,G.F.(2010).Abriefintroductiontotheuse ofeventrelatedpotentialsinstudiesofperception andattention.Attention,Perception&Psychophysics, 72(8),20312046.
Today
Electroencephalogram(EEG) IntroductiontoEEGandrecording EEGartifacts ExaminingarealEEGdataset Homework1
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Background
Electroencephalogram (EEG)
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Electroencephalogram (EEG)
Electroencephalogram (EEG)
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Electroencephalogram (EEG)
EEG
EEGmeasurestheactivityoflargenumbers (populations)ofneurons Scalp EEGrecordingsarenoninvasive,painless,do notinterferemuchwithahumansubjectsabilityto moveorperceivestimuli,arerelativelylowcost: researchandclinicalgoals IntracranialEEGrecordingsareinvasiveandareonly usedtolocalizeepilepticfociinpatientswithepilepsy thatcannotbemanagedwithmedications: mostlyclinicalgoals
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EEG
Mid1920s:developed human electroencephalography Followedthestudiesof RichardCatoninnon humananimalspecies. Describedthehuman alphaandbetarhythms
HansBerger
EEG
Reference electrodes
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Collecting EEG
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EEG amplifiers
9V 1.5V
50V
1V=1millionthofaVolt!
EEG amplifiers
Theolddays
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EEG amplifiers
Thesedays 2cm
10cm
EEG Electrodes
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EEG Methods
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EEG montages
32electrodes
EEG montages
64electrodes
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EEG rhythms
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EEG rhythms
EEGgoodindicatorofglobalbrainstate EEGoftendisplaysrhythmicpatternsatcharacteristic frequencies Alpha() 813Hz 2060V Occipital
200uV 200uV
1s
EEG rhythms
1s
Mostcommonbrainrhythm Thought&mentalactivity
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EEG rhythms
200uV 200uV
1s
EEG rhythms
1s
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EEG rhythms
200uV
1s
EEG rhythms
GammaWaves KappaWaves LambdaWaves MuWaves
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Intracranial EEG
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EEG in epilepsy
absence seizure
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EEG in epilepsy
Generalized spikeand wave discharges
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Inverse problem
many <= one (easy) many => one (hard)
Limited spatial resolution: need additional information to more precisely estimate location of neural sources
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EEG Artifacts
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50/60 Hz
50/60Hznoise
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Amplifier blocking
Signalgoesbeyondthe dynamicrangeofthe amplifier(e.g. dueto slowlyvaryingskin potentials,movement)
Eye Artifacts
Blinks & Saccades Eyeactslikeabattery:corneaiselectricallypositiverelativeto backoftheeye(EmilduBoisReymond,1848)
CORNEA
+
RETINA
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Eye Artifacts
Blinks & Saccades Basicallytheeyeisanelectricaldipole Corneoretinalpotentialsareabout1mV Brainpotentialsatscalpare1000timessmaller(1V) Asyoumoveyoureyesaroundyouchangetheorientationof thedipoleandthedistributionofpotentialoverthehead Blinksarealsoaproblembecausetheeyelidschangethe electricalpropertiesoftheeye
Blinks
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Saccades
(eye movements: Electro-oculogram [EOG]) EEG is a cheap way to measure eye movements!
Saccades
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Skin potentials/sweat
(skin conductance response [SCR]) Skinpotentialscanproduce slowfluctuationsintheEEG signal,oftenresultingalsoin blocking
Skin potentials/sweat
skin potentials
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Skin potentials/sweat
skin potentials
Cardiac artifacts
(Electrocardiogram [EKG])
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Muscle artifacts
(Electromyogram [EMG])
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Alpha Rhythm
Alpha
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Alpha
Artifacts
(in order of insidiousness, from worst to least bad) 1. 2. 3. 4. 5. 6. 7. 8. Environmental electromagnetic field (EMF) noise Blocking (flatline: Reduced/No EEG!) Blinks Saccades Skin potentials (skin conductance response [SCR]) Electrocardiogram (EKG) Electromyogram (EMG) Alpha
Subject controlled (but experimenter can influence) Experimenter controlled (even if subject is the source)
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Custom montage
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Experiment
Nonconscious (implicit) memory. Can we detect memory in the brainwaves even when people consciously deny having it? Materials: Pictures of new and repeated objects EEG for each picture is tagged with an event code. Our event codes: 111-117, 131-137 Goal: Process data to obtain a valid event-related potential for each subject (next weeks topic) Today (and in Homework1) we examine the raw EEG to make sure we get rid of artifacts so later we can produce good valid ERPs from the data
Files you need are in the Psy250_Analysis directory on your usb key. To see the full filenames, do the following: Double click Psy250_Analysis to open it in windows explorer on your usb key In windows explorer, Click Tools menu. Choose Folder Options Click on the View tab Under Advanced settings: Uncheck Hide extensions for known file types. OK
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Software 1. MATLAB start/All Programs/MATLAB >> eeglab<Enter> 2. EEGLab tool for Matlab http://sccn.ucsd.edu/eeglab/ 3. ERPLab plugin for EEGLab http://erpinfo.org/erplab http://erpinfo.org/erplab/erplab-documentation http://erpinfo.org/erplab/erplab-documentation/manual ERPLAB menu EEGLAB File/Load existing dataset Plot/channel data (scroll) Display/Remove DC offset Analysis_Files bdf/UsUnIE-imp-bdf-rts.txt AddBlinkCh65.txt
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Steps already done for you: 1. Create Event List ERPLAB > EventList > Create EEG EventList (basic or advanced)
Choose: basic Example eventlist text output in eventlist directory (subject # 39)
Assign Events to Bins of Experimental Conditions ERPLAB > Assign Bins (BINLISTER) Load Bin Descriptor File from: Your directory\bdf\UsUnIE-impbdf-rts.txt Read EventList from Check: Current dataset: UsUnIE39-imp_elistnor_e64M2.set Write resulting EventList to Check: Current dataset Check: Text file (e.g., UsUnIE39-imp_elist Check: Transfer nor_e64M2-blf.txt) EVENTLIST.eventinfo info to Check: Create detailed EEG.event (for plotting and other report EEGLAB functions) Uncheck: Matlab workspace Uncheck: Reset Artifact Flags (as EVENTLIST variable) Uncheck: Reset User Flags Hit: Run
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Assign Events to Bins of Experimental Conditions ERPLAB > Assign Bins (BINLISTER) Load Bin Descriptor File from: Your directory\bdf\UsUnIE-impbdf-rts.txt Read EventList from Check: Current dataset: UsUnIE39-imp_elistnor_e64M2.set Write resulting EventList to Check: Current dataset Check: Text file (e.g., UsUnIE39-imp_elistnor_e64M2-blf.txt) Check: Create detailed report Uncheck: Matlab workspace (as EVENTLIST variable)
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Assign Events to Bins of Experimental Conditions ERPLAB > Assign Bins (BINLISTER) . (continued) Events to use as TYPE: Numeric Codes Hit: APPLY What do you want to do with the new dataset? Name it (accept default): datasetname_elist_nelist Check: Save it as file UsUnIE39-imp_elistnor_e64M2_nelist What do you want to do with the old dataset? Check Overwrite it in memory. Hit: Ok Output: dataset (-blf, -blf_REPORT move these text files to bdf dir)
http://erpinfo.org/erplab/erplabdocumentation/manual/Binlister.html
Assign Events to Bins of Experimental Conditions ERPLAB > Assign Bins (BINLISTER). (continued) Events to use as TYPE: Numeric Codes Hit: APPLY What do you want to do with the new dataset? Name it (accept default): datasetname_elist_nelist Check: Save it as file Copy name, browse to your directory and paste UsUnIE39imp_elist-nor_e64M2_nelist What do you want to do with the old dataset? Check Overwrite it in memory. Hit: Ok Output: dataset (-blf, -blf_REPORT move these text files to bdf dir)
http://erpinfo.org/erplab/erplabdocumentation/manual/Binlister.html
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Assign Events to Bins of Experimental Conditions ERPLAB > Assign Bins (BINLISTER). (continued) Events to use as TYPE: Numeric Codes Hit: APPLY What do you want to do with the new dataset? Name it (accept default): datasetname_elist_nelist Check: Save it as file Copy name, browse to your directory and paste UsUnIE39imp_elist-nor_e64M2_nelist What do you want to do with the old dataset? Check Overwrite it in memory. Hit: Ok Output: dataset (-blf, -blf_REPORT move these text files to bdf dir)
http://erpinfo.org/erplab/erplabdocumentation/manual/Binlister.html
Extract Bin Epochs Divide continuous EEG into epochs (time periods) for each trial in a bin (i.e., an experimental condition) ERPLAB > Extract Bin-Based Epochs Bin-based epoch time range (ms): -200 800 Check Baseline correction Pre Hit: RUN What do you want to do with the new dataset? Name it (accept default) Check: Save it as file UsUnIE39-imp_elistnor_e64M2_nelist_be What do you want to do with the old dataset? Check Overwrite it in memory Hit: Ok EEGLAB: Plot/channel data (scroll)
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Bins 3 and 23
Epoch
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Add channel(s) for artifact detection ERPLAB > EEG Channel Operations
Check Create new dataset Check Warn if channels will be overwritten Equation List Click Load list Choose AddBlinkCh65.txt Adds channel 65 and Computes as blink channel nch65 = ch1 - ch6 label Blink (channel 1 = right LE, channel 6 = right Fp) Hit: RUN
Add channel(s) for artifact detection ERPLAB > EEG Channel Operations
Check Create new dataset Check Warn if channels will be overwritten Equation List Click Load list Choose AddBlinkCh65.txt Adds channel 65 and Computes as blink channel nch65 = ch1 - ch6 label Blink (channel 1 = right LE, channel 6 = right Fp) Hit: RUN
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Add channel(s) for artifact detection ERPLAB > EEG Channel Operations What do you want to do with the new dataset? Name it (accept default): datasetname_elist_nelist_be6 5 (all 64 recorded chans plus blink ch # 65) Check: Save it as file UsUnIE39-imp_elistnor_e64M2_nelist_be65.set What do you want to do with the old dataset? Check Overwrite it in memory. Hit: Ok EEGLAB/Plot/Channel data(scroll) verify added channel 65 Blink
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Add channel(s) for artifact detection ERPLAB > EEG Channel Operations
Add channel(s) for artifact detection ERPLAB > EEG Channel Operations
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Add channel(s) for artifact detection ERPLAB > EEG Channel Operations
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Get Artifact Rejection Values (GARV) 1) Find EEG segments with artifacts so we can get rid of them: Artifact Detection 2) Determine value of thresholds for detecting each type of artifact 3) Mark epochs with artifacts 4) Save dataset with marked artifacts
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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Artifact Detection Functions Vertical Saccade / vertical electrooculogram ERPLAB/Artifact Detection/Moving Window Peak-to-Peak threshold Mark flag 4 Test period = -200.0 795.0 Garv: Voltage threshold (microvolts) = 100 Moving Windows Full Width (ms) = 200 Window Step (ms) = 50 Channels = 1 (LE) Accept GARV to assess. Record epoch # of H & FA for each threshold Cancel and Repeat until voltage threshold determined If garv successful, then, as elsewhere, Name, save new dataset as_arBloBliEog, overwrite old. Ok.
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
Artifact Detection Functions Vertical Saccade / vertical electrooculogram ERPLAB/Artifact Detection/Moving Window Peak-to-Peak threshold
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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Artifact Detection Functions Vertical Saccade / vertical electrooculogram ERPLAB/Artifact Detection/Moving Window Peak-to-Peak threshold
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
Artifact Detection Functions Vertical Saccade / vertical electrooculogram ERPLAB/Artifact Detection/Moving Window Peak-to-Peak threshold
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Artifact Detection Functions Horizontal Saccade / Horizontal electrooculogram ERPLAB/Artifact Detection/ Step-like artifacts
Mark flag 5 Test period = -200.0 795.0 Garv: Voltage threshold (microvolts) = 25 Moving Windows Full Width (ms) = 400 Window Step (ms) = 10 Channels = 2 (HE) Accept GARV to assess. Record epoch # of H & FA for each threshold Cancel and Repeat until voltage threshold determined If garv successful, then, as elsewhere, Name, save new dataset as_arBloBliEogHe, overwrite old. Ok.
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
Artifact Detection Functions Horizontal Saccade / Horizontal electrooculogram ERPLAB/Artifact Detection/ Step-like artifacts
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
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Artifact Detection Functions Horizontal Saccade / Horizontal electrooculogram ERPLAB/Artifact Detection/ Step-like artifacts
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html
Artifact Detection Functions Horizontal Saccade / Horizontal electrooculogram ERPLAB/Artifact Detection/ Step-like artifacts
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MATLAB window record % Rejected trials If > 33% rejected, then exclude subject (Picton et al 2000)
Homework 1
Do the same with your own subject. GARV: Get artifact detection values for blocks, blinks, and saccades that work well for that subject. Using an Excel spreadsheet, keep track of epoch # of Hits and False Alarms and % rejected for each threshold that you try. Use a different spreadsheet for each type of artifact. Expect to reject a total of 5-15 trials (out of a total of 35). Number varies by subject. Next week: We will use the artifact detection values to average the data. We will also check that no major artifacts were included in the average, and no good data were rejected. Remember to bring your USB stick!
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PALS
PALSareagreatvenueforstudents tofurtherexploreissuesdiscussed Sessionsarestudentledandthus thestudentsdecidewhattocover
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Create Event List Identifies critical events in the EEG ERPLAB > EventList > Create EEG EventList Basic Export EventList to text file (Browse to data directory,
and enter filename: UsUnIE39_EventListText)
Add code -99 CREATE Save it as file: UsUnIE39imp_elist-nor_e (Browse to data directory) Overwrite it in memory Ok
Delete channels not needed, if any Dataset: UsUnIE39imp_elist-nor_e EEGLAB>Edit>Select data Channel range Input desired range = 65:68 check on->remove these Ok Save as 64 (e.g., UsUnIENNimp_elist-nor_e64.set)
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Add Channel Locations EEGLAB>Edit>Channel locations To load a channel locations file, press the Read Locations button and select the channel locations file in Matlab .xyz file format: geodesic-mod-eeglab_64M2.xyz Name, Save as new filename_elist-nor_e64M2, overwrite old dataset, as usual
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