10/9/2012

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)

Graphic representationofthe difference

Electroencephalogram (EEG)

Graphic representationofthe differenceinvoltage betweentwo different

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Electroencephalogram (EEG)

Graphic representationofthe differenceinvoltage betweentwo differentcerebral locationsplottedover time

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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Continuous EEG recording

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

Electrodes:Tin,Ag/AgCl,gold EEGelectrodes:Attachedtothe scalp Referenceelectrodes:Mastoid, nose,earlobe

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EEG Conduction from Scalp to Electrode

Conductivegel

EEG Methods

Someinexpensivegadgets,butLowqualitysignals(notgoodfor mostresearchpurposes) Perhapsgoodenoughforbinarychoices(e.g.,moveleft/right) ManycompaniesclaimtheyuseEEGtocontrolvideogamesIn reality,mostlytheypickuplargemuscleandeyemovementsignals!

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10-20 electrode position system

Standardplacementsofelectrodesonthehumanscalp:A, auricle;C,central;F,frontal;Fp,frontalpole;O,occipital;P, parietal;T,temporal.Odd/evenconvention.

Recording EEG: caps

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EEG montages
32electrodes

EEG montages
64electrodes

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10-10 electrode position system

(high-density)

Standardplacementsofelectrodesonthehumanscalp:A, auricle;C,central;F,frontal;Fp,frontalpole;O,occipital;P, parietal;T,temporal&combinedAF,CP,PO,TP.Odd/even convention.

10-5 electrode position system

(high-density)

Standardplacementsofelectrodesonthehumanscalp:A, auricle;C,central;F,frontal;Fp,frontalpole;O,occipital;P, parietal;T,temporal&combinedAF,CP,PO,TP&combined+ half(AFF,FCC,CCP,PPO,POO+h).Odd/evenconvention.

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How many electrodes?

Dependsonthequestionofinterest 64 or more Less than 64 Longer set up Shorter set up Better characterize Detect broadly distributed broadly distributed effects effects Likely to miss focal Likely to detect focal No or poor estimate of Valid estimate of brain sources brain sources
More valid common average reference (i.e., reference free assumption more valid) Montage-dependent common average reference (i.e., violate reference free assumption)

Can discover new effect at new location

Requires predicting a priori which electrodes show effect

EEG rhythms

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EEG rhythms
EEGgoodindicatorofglobalbrainstate EEGoftendisplaysrhythmicpatternsatcharacteristic frequencies Alpha() 813Hz 2060V Occipital

200uV 200uV

1s

Easilyproducedwhenquietlysittinginrelaxedpositionwith eyesclosed(fewpeoplehavetroubleproducingalphawaves) Alphablockadeoccurswithmentalactivity

EEG rhythms

Beta() 1330Hz 220V Parietal/Frontal

1s

Mostcommonbrainrhythm Thought&mentalactivity

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EEG rhythms

200uV 200uV

Theta() 48Hz 2o10oV

1s

Morecommoninchildrenthanadults Maulsby(1971)foundthetawaveswithamplitudesof100Vin babiesfeeding Associatedwithmedialtemporallobememoryfunction

EEG rhythms

Delta() 0.54Hz 2o20oV

1s

Deepsleepinmostpeople Characterizedbyveryirregularandslowwavepatterns Detecttumors&abnormalbrainactivity

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EEG rhythms

200uV

Spikes 3Hz Epilepsy Petit mal

1s

EEG rhythms
GammaWaves KappaWaves LambdaWaves MuWaves

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Intracranial EEG

Intracranial EEG in epilepsy

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Intracranial EEG in epilepsy

Grand mal epileptic seizure

EEG in epilepsy
absence seizure

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EEG in epilepsy
Generalized spikeand wave discharges

Neural basis of EEG

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Neural basis of EEG

Neural basis of EEG

ManyneuronsmustsumactivitytodetectwithEEGelectrodes Timingofneuralactivitycrucial Synchronizedneuralactivityproduceslargersignals Orientation&spatialdistributionofneuralactivitycrucial

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What does the EEG record?

Volume Conduction Electricalactivityflowsthrough thetissuebetweentheelectrical generatorandrecordingelectrode Hightimeresolution(1ms) Thus EEG is a 2D representation of a 3D reality, which poses a problem for localizing the sources of the electrical activity: Inverse problem

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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Quality control of EEG recording

EEG amplifiers must be calibrated with daily checks (mostly with old equipment) Acquisition parameters must be checked daily and kept the same Same procedures must be used in all subjects All artifacts must be removed or taken into account prior to analysis
Reject all trials with artifacts or filter artifacts (introduces bias and/or distortion)

Electromagnetic field (EMF) noise

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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(eye movements: Electro-oculogram [EOG])

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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Cardiac artifacts (EKG)

Cardiac artifacts (EKG)

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Muscle artifacts
(Electromyogram [EMG])

Muscle artifacts (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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Lets examine some EEG data

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)

2. Remove channels not analyzed

EEGLAB>Edit>Select data> Channel range 65:69

3. Channel locations added EEGLAB>Edit>Channel locations

Example .xyz file in channel_locations directory
http://erpinfo.org/erplab/erplabdocumentation/manual/EventList_Create.html

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

Time window ofinterest

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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

Blink = (LE 2) Ch # 65 = (ch #1 ch #6)

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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

Artifact Detection Functions for Blocking Blinks Saccades Other

http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html

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Artifact Detection Functions Blocking

ERPLAB/Artifact Detection/Blocking & Flatline (alpha) Mark flag 2 (mark 1 is always set by ERPLab) Test period = your entire epoch = -200.0 795.0 Amplitude tolerance = 2 Garv: Duration (ms) = 60 Channels = 1:3 5:64. All channels, except added blink channel (#65) and nose (#4 not analyzed) Hit: Accept Scroll to verify 100% hits & 0 false alarms Record epoch # of H & FA for each threshold If garv no good, then Cancel & repeat If garv successful, then, as before: Name (_arBlo), Save new, Overwrite old. Ok
http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html

Artifact Detection Functions Blocking

ERPLab/Artifact Detection/Blocking & Flatline (alpha)

http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html

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Artifact Detection Functions Blocking

ERPLab/Artifact Detection/Blocking & Flatline (alpha)

http://erpinfo.org/erplab/erplab-documentation/manual/Artifact_Detection.html

Artifact Detection Functions

ERPLab/Artifact Detection/Blocking & Flatline (alpha).

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Artifact Detection Functions

Blinks ERPLAB/Artifact Detection/Step-like artifacts Mark flag 3 Test period = -200.0 795.0 Garv: Voltage threshold (microvolts) = 40 Moving Windows Full Width (ms) = 400 Window Step (ms) = 10 Channels = 65 (Blink channel #) 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_arBloBli, overwrite old. Ok.
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

Artifact Detection Functions

Blinks ERPLAB/Artifact Detection/Step-like artifacts

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

Steps done already

For information only (optional)

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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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