Presentation is loading. Please wait.

Presentation is loading. Please wait.

EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 1 Using EEGLAB history for basic scripting EEG.history.

Published byRussell Norman Modified over 8 years ago

Similar presentations

Presentation on theme: "EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 1 Using EEGLAB history for basic scripting EEG.history."— Presentation transcript:

1 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 1 Using EEGLAB history for basic scripting EEG.history  useful information Task 1 Create simple script using 'eegh' Exercise... Task 2 Eye-blink correction Create a new EEG field Exercise... Task 3 Script to process multiple data sets Exercise...

2 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 2 The example data: faces vs. objects Data 33 channel EEG, nose-tip reference, 250 Hz sampling rate, 0.5-100 Hz, 16 bit, BrainAmps Task speeded discrimination between objects and faces, 500 ms presentation duration, ISI 500-1900 ms, 362 trials

3 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 3 Using EEGLAB history for basic scripting EEG.history  useful information Task 1 Create simple script using 'eegh' Exercise... Task 2 Eye-blink correction Create a new EEG field Exercise... Task 3 Script to process multiple data sets Exercise...

4 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 4 Task 1: Load dataset >> EEG.history How do I retrieve information about the processing history of a data set?

5 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 5 EEG.history >> EEG.history ans = EEG = pop_loadbv('.../data/rawdata/', 'faces_4.vhdr'); EEG.setname='faces_4_continuous'; EEG = eeg_checkset( EEG ); EEG.chanlocs=pop_chanedit(EEG.chanlocs, 'load',[],... 'load',{ '.../wsporto/data/chan_locs.elp', 'filetype',... 'besa (elp)'}, 'eval',... 'chantmp = pop_chancenter( chantmp, [],[]);'); EEG = pop_saveset( EEG, 'faces_4.set', '.../workshop/'); EEG = pop_multifit(EEG, [1:33], 'settings',{},'threshold',... 40, 'plotopt',{ 'normlen', 'on', 'image','fullmri'}); pop_topoplot(EEG,0, [1:12], 'faces_4 continuous',... [3 4],0, 'electrodes', 'off', 'masksurf', 'on'); % no history for manual DIPFIT dipole localization EEG = pop_saveset( EEG, 'faces_4.set', '.../workshop/');

6 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 6 Using EEGLAB history for basic scripting EEG.history  useful information Task 1 Create simple script using 'eegh' Exercise... Task 2 Eye-blink correction Create a new EEG field Exercise... Task 3 Script to process multiple data sets Exercise...

7 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 7 Task 1: Load dataset

8 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 8 Task 1: Plot ERPimage

9 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 9 Task 1: Resulting figure

10 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 10 Script task 1 using 'eegh' >> eegh How do I write a script to do this?

11 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 11 Script task 1 using 'eegh' >> eegh [ALLEEG EEG CURRENTSET ALLCOM] = eeglab; EEG = pop_loadset('filename','faces_4.set','filepath',... '...\data\'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 0); EEG = pop_epoch( EEG, { 'face' 'object' }, [-0.2 0.8],... 'newname', 'faces_4 epochs', 'epochinfo', 'yes'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1); EEG = pop_rmbase( EEG, [-200 0]); [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); figure; pop_erpimage(EEG,1, [21],[],'e21',10,1,{},[],... '','yerplabel','\muV','topo',... { [21] EEG.chanlocs EEG.chaninfo },'erp','cbar');

12 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 12 Script task 1 using 'eegh' % open Matlab editor: >> edit % copy & paste eegh results into a new % file and save it (../faces1.m) % type faces1 on Matlab command line >> faces1

13 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 13 Exercise >> eeglab % repeat all steps of task 1: % load dataset, % epoch on 'face' and 'object' % plot erpimage for any channel >> eegh % open Matlab editor: >> edit % copy & paste eegh results into a new % file and save it (../faces1.m) >> clear >> close all >> faces1

14 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 14 Using EEGLAB history for basic scripting EEG.history  useful information Task 1 Create simple script using 'eegh' Exercise... Task 2 Eye-blink correction Create a new EEG field Exercise... Task 3 Script to process multiple data sets Exercise...

15 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 15 Eye blink correction How do you identify eye-blink components?

16 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 16 Eye blink correction

17 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 17 Eye blink correction

18 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 18 Eye blink correction

19 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 19 Eye blink correction Trial 43: Fp1/2 before (b) and after (r) correction ICA-based eye blink correction is great!

20 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 20 Task 3: Scripting ICA eye blink correction

21 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 21 Task 3: Scripting ICA eye blink correction EEGLAB structure can be extended to include new fields -Useful procedure to store information that may be accessed in future scripts Write a semi-automatic script to save eye blink IC index as EEG.blink How do I create a new EEG structure field?

22 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 22 Task 3: Scripting ICA eye blink correction % faces2.m % infile = 'faces_3.set'; % define input.set file inpath = '...\data\'; % define input directory % start eeglab [ALLEEG EEG CURRENTSET ALLCOM] = eeglab; % load data set EEG = pop_loadset(infile, inpath); [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG); % plot IC maps pop_topoplot(EEG,0, [1:size(EEG.data,1)],infile,... [6 6],0,'electrodes', 'off', 'masksurf', 'on'); 

23 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 23 Task 3: Scripting ICA eye blink correction % faces2.m (cont'd) % Enter eye blink indices manually EEG.blink = input('Enter eye blink component indices: '); % save info in current data set EEG = pop_saveset(EEG, infile, inpath); [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); % update EEGLAB gui eeglab redraw;

24 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 24 Exercise: Script it yourself! % faces2.m infile = 'faces_3.set'; inpath = '...\data\'; % start eeglab [ALLEEG EEG CURRENTSET ALLCOM] = eeglab; % load data set EEG = pop_loadset(infile, inpath); [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG); % plot IC maps pop_topoplot(EEG,0, [1:size(EEG.data,1)],infile,... [6 6],0,'electrodes', 'off', 'masksurf', 'on'); % Enter eye blink indices manually EEG.blink = input('Enter eye blink component indices:'); % save info in current data set EEG = pop_saveset(EEG, infile, inpath); [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); eeglab redraw;

25 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 25 Using EEGLAB history for basic scripting EEG.history  useful information Task 1 Create simple script using 'eegh' Exercise... Task 2 Eye-blink correction Create a new EEG field Exercise... Task 3 Script to process multiple data sets Exercise...

26 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 26 Task 4: Loop across data sets From the gui, perform the following operations: 1) Load the dataset 2) Subtract ICA eye blink component activity 3) Epoch data (-200 to 800 ms) on object and face events 4) Compare the ERPs of both conditions * Use: Plot  Sum/Compare ERPs 5) Use 'eegh' to retrieve commandline functions THEN: Write a script doing all this automatically ** Use a for loop and variables for maximum efficiency How do I compare two conditions from the same session?

27 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 27 Task 4: GUI functions (review)

28 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 28 Task 4: GUI functions, cont'd

29 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 29 Task 4: GUI functions, cont'd

30 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 30 Task 4: GUI functions, cont'd

31 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 31 Task 4: Matlab commandline output >> pop_loadset(): loading file …/faces_4.set... eeg_checkset: recomputing the ICA activation matrix... Creating a new ALLEEG dataset 1 Done. Computing projection.... Components removed eeg_checkset: recomputing the ICA activation matrix... Done. pop_epoch():364 epochs selected Epoching... pop_epoch():364 epochs generated eeg_checkset: recomputing the ICA activation matrix... pop_epoch(): checking epochs for data discontinuity Done. pop_rmbase(): Removing baseline... eeg_checkset: recomputing the ICA activation matrix... Done. Removing 182 trial(s)... Pop_select: removing 359 unreferenced events Creating a new ALLEEG dataset 2 Done. Removing 182 trial(s)... Pop_select: removing 366 unreferenced events Creating a new ALLEEG dataset 3 Done. eegh

32 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 32 Task 4: eegh history output >> eegh [ALLEEG EEG CURRENTSET ALLCOM] = eeglab; EEG = pop_loadset( 'filename', 'faces_4.set', 'filepath', '…\data\' ); [ALLEEG, EEG, CURRENTSET] = eeg_store( ALLEEG, EEG, 0 ); EEG = pop_subcomp( EEG, [4], 0); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1, 'setname',… 'faces_4 pruned with ICA', 'overwrite', 'on'); EEG = pop_epoch( EEG, { 'face' 'object' }, [-1 2], 'newname',… 'faces_4 pruned with ICA epochs', 'epochinfo', 'yes'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1, 'overwrite', 'on'); EEG = pop_rmbase( EEG, [-200 0]); [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); EEG = pop_selectevent( EEG, 'type',{ 'face' }, 'deleteevents','off',… 'deleteepochs', 'on'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1, 'setname', 'faces only epochs' ); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 2, 'retrieve',1, 'study',0); EEG = pop_selectevent( EEG, 'type',{ 'object' }, 'deleteevents', 'off',… 'deleteepochs', 'on'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1, 'setname', 'object only epochs' );

33 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 33 Task 4: Create a script % load data set indata = 'faces_4.set'; % replace strings inpath = '...\data\'; % with variables EEG = pop_loadset( indata,inpath); [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG,1); % remove eye components for ERP plotting % replace IC index with your new EEG field: EEG = pop_subcomp( EEG, EEG.blink, 0); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG,… EEG, 1, 'overwrite', 'on'); % Epoch the data -- replace events with a variable condition={'object','face'}; EEG=pop_epoch( EEG,condition,[-0.2 0.8],… 'epochinfo','yes'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,… 'overwrite','on'); % still in ALLEEG(1) EEG = pop_rmbase( EEG, [-200 0]); [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET);

34 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 34 Task 4: Create a script, cont'd % Create 'face-only dataset EEG = pop_selectevent( EEG, 'type',{condition{1}},… 'deleteevents', 'off', 'deleteepochs', 'on'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,… 'setname', condition{1}); % Retrieve original epoched dataset [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 2,… 'retrieve',1, 'study',0); % Create 'object'-only dataset EEG = pop_selectevent( EEG, 'omittype',{condition{2}},… 'deleteevents', 'off', 'deleteepochs', 'on'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1, … 'setname', condition{2});

35 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 35 Task 4: Loop across data sets % create datasets for each condition for i = 1:length(condition) EEG = pop_selectevent(EEG,'type',{condition{i}},... 'deleteevents','off','deleteepochs','on'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,... 'setname', condition{i}); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, i+1,… 'retrieve',1, 'study',0); % Go back to ALLEEG(1) end % plot ERPs pop_comperp( ALLEEG, 1, [2 3],[],'addavg', 'off',... 'addstd','off', 'addall', 'on', 'diffavg','off',... 'diffstd','off', 'tplotopt',{'title',... 'Object vs Face ERPs', 'ydir', -1}); % save figure; print('-dtiff', [inpath,'erp.tif']);

36 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 36 Task 4: Loop across data sets Face vs Object ERPs

37 EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 37 Exercise: Script it yourself! % replace strings with variables indata = 'faces_4.set'; inpath = '...\data\'; condition = {'object','face'}; %-------------------------------------------------------------------- EEG = pop_loadset( indata,inpath); [ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG); EEG = pop_subcomp( EEG, EEG.blink, 0); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG,EEG, 0, 'overwrite', 'on'); EEG=pop_epoch( EEG,{condition},[-0.2 0.8],… 'epochinfo','yes'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,'overwrite','on'); EEG = pop_rmbase( EEG, [-200 0]); [ALLEEG EEG] = eeg_store(ALLEEG, EEG, CURRENTSET); for i = 1:length(condition) EEG = pop_selectevent(EEG,'type',{condition{i}},'deleteevents','off','deleteepochs','on'); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,CURRENTSET, 'setname', condition{i}); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, i+1,'retrieve',1, 'study',0); end pop_comperp( ALLEEG, 1, [2 3],[],'addavg', 'off',... 'addstd','off', 'addall', 'on', 'diffavg','off',... 'diffstd','off', 'tplotopt',{'title',... 'Object vs Face ERPs', 'ydir', -1}); print('-dtiff', [inpath,'erp.tif']); Example script saved as: '…/Scripts/practicum_4.m'

Download ppt "EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – Using EEGLAB history for basic scripting 1 Using EEGLAB history for basic scripting EEG.history."

Similar presentations

System Integration and Performance

System Integration and Performance
Measure Projection Analysis: Practicum

Measure Projection Analysis: Practicum
NEMO ERP Analysis Toolkit ERP Metric Extraction An Overview.

NEMO ERP Analysis Toolkit ERP Metric Extraction An Overview.
Introduction to Matlab

Introduction to Matlab
Introduction to Matlab Workshop Matthew Johnson, Economics October 17, 2008 4/13/20151.

Introduction to Matlab Workshop Matthew Johnson, Economics October 17, /13/20151.
Introduction to MATLAB for Biomedical Engineering BME 1008 Introduction to Biomedical Engineering FIU, Spring 2015 Lesson 2: Element-wise vs. matrix operations.

Introduction to MATLAB for Biomedical Engineering BME 1008 Introduction to Biomedical Engineering FIU, Spring 2015 Lesson 2: Element-wise vs. matrix operations.
Microsoft Visual Basic: Reloaded Chapter Seven More on the Repetition Structure.

Microsoft Visual Basic: Reloaded Chapter Seven More on the Repetition Structure.
Why python? Automate processes Batch programming Faster Open source Easy recognition of errors Good for data management What is python? Scripting programming.

Why python? Automate processes Batch programming Faster Open source Easy recognition of errors Good for data management What is python? Scripting programming.
Week 6 - Programming I So far, we’ve looked at simple programming via “scripts” = programs of sequentially evaluated commands Today, extend features to:

Week 6 - Programming I So far, we’ve looked at simple programming via “scripts” = programs of sequentially evaluated commands Today, extend features to:
EEGLAB Workshop III, Nov. 15-18, 2005, Singapore: Julie Onton – Artifact processing and ERP analysis 1 Artifact processing and ERP analysis Task 1 Reject.

EEGLAB Workshop III, Nov , 2005, Singapore: Julie Onton – Artifact processing and ERP analysis 1 Artifact processing and ERP analysis Task 1 Reject.
Introduction to MATLAB Northeastern University: College of Computer and Information Science Co-op Preparation University (CPU) 10/22/2003.

Introduction to MATLAB Northeastern University: College of Computer and Information Science Co-op Preparation University (CPU) 10/22/2003.
Lecture 7 Sept 17 Goals: Complete Chapter 4 Chapters 5 and 6.

Lecture 7 Sept 17 Goals: Complete Chapter 4 Chapters 5 and 6.
Week 6 - Programming I So far, we’ve looked at simple programming via “scripts” = programs of sequentially evaluated commands Today, extend features to:

Week 6 - Programming I So far, we’ve looked at simple programming via “scripts” = programs of sequentially evaluated commands Today, extend features to:
Lecture 7 Sept 29 Goals: Chapters 5 and 6. Scripts Sequence of instructions that we may want to run can be stored in a file (known as script). by typing.

Lecture 7 Sept 29 Goals: Chapters 5 and 6. Scripts Sequence of instructions that we may want to run can be stored in a file (known as script). by typing.
Introduction to MATLAB Northeastern University: College of Computer and Information Science Co-op Preparation University (CPU) 10/22/2003.

Introduction to MATLAB Northeastern University: College of Computer and Information Science Co-op Preparation University (CPU) 10/22/2003.
Division Example 2x - 3y + 4z = 10 x + 6y - 3z = 4 -5x + y + 2z = 3 A*X = B where A = 2 -3 4 1 6 -3 -5 1 2 B = 10 4 3 >> X = A\B X = 1.2609 2.2261 3.5391.

Division Example 2x - 3y + 4z = 10 x + 6y - 3z = 4 -5x + y + 2z = 3 A*X = B where A = B = >> X = A\B X =
Session Management A290/A590, Fall 2014 09/25/2014.

Session Management A290/A590, Fall /25/2014.
EEGLAB Workshop III, Nov. 15-18, 2006, Singapore: Julie Onton – DIPFIT and model co-registration 1 DIPFIT and model co-registration Task 1 Co-register.

EEGLAB Workshop III, Nov , 2006, Singapore: Julie Onton – DIPFIT and model co-registration 1 DIPFIT and model co-registration Task 1 Co-register.
ME457 Mechatronic System Modeling MICHIGAN STATE UNIVERSITY Matlab® refresher Your objective: to dominate! My objective: to help you dominate!

ME457 Mechatronic System Modeling MICHIGAN STATE UNIVERSITY Matlab® refresher Your objective: to dominate! My objective: to help you dominate!
1 An Introduction to TI SmartView Emulator Software (Version 2.0) Jim Eiting Developmental Mathematics Department Collin County Community College August.

1 An Introduction to TI SmartView Emulator Software (Version 2.0) Jim Eiting Developmental Mathematics Department Collin County Community College August.

Similar presentations

Ads by Google