[Eeglablist] script example, to extract epochs?

[Hamish INNES-BROWN]

Memory always seems to be an issue.  I've heard using 64-bit matlab will
help, but that might not be possible (it's not for me at least), so here
is my solution (it's not pretty I admit): I try and do everything in
small steps, but all the subjects at once, restarting matlab when it
crashes and picking up where it left off... ie I do all the epoching in
one script (for all the subjects), then all the re-referencing in
another, and so on.  

Matlab is bound to crash (memory), and the only solution seems to be to
actually restart matlab (the pack command doesn't do much, clear and
restart eeglab doesn't work either). So I have the "input files" in one
directory ('rawpath' in the script below), then the output files go into
a separate directory ('savepath'). When matlab inevitabley runs out of
memory on a bigger-than-usual .set file, it crashes, and I just look in
the 'savepath' directory and see where it got up to.  I then have a 3rd
directoy called "finished" - I move the sucessfully processed .set files
into the "finished" directory (usually just by hand in windows), then
run the script again. The script works by finding a list of files in the
raw directory, so once the processed files are moved out of there, it no
longer sees them, and starts at the next un-processed file. 

So far I've been lucky, my files are just small enough that restarting
matlab freshly will allow them to be epoched, but some of them wont
epoch if anything else has been opened first. Seems the .set file can be
up to around 150MB for me.

Like I said, it's not an elegant solution, but as you mentioned the
memory issue only appeared on the 2nd time around the loop, I thought
this might be the same problem.  

(this is for epoching continuous data, but I guess the principle is the
same)


If anyone has a more elegant solution I'd also be glad to hear it.




% Matlab script for epoching all the set files

% 1) get list of set files in raw data directory

rawpath =  'D:\_PROJECTS\_FB\_ANALYSIS\__EEGLAB\SET\01raw\';
savepath = 'D:\_PROJECTS\_FB\_ANALYSIS\__EEGLAB\SET\02epochs\';
triggers = {'111' '122' '131' '141' '142' '151' '152' '162'};

cd(rawpath);
files = dir('*.set');
nfiles = size(files,1);


for i = 1:nfiles
    %[ALLEEG EEG CURRENTSET ALLCOM] = eeglab;

    EEG = pop_loadset( 'filename', files(i).name, 'filepath', rawpath);
    EEG = eeg_checkset( EEG );
    [ALLEEG EEG CURRENTSET ] = eeg_store(ALLEEG, EEG);
    EEG = pop_epoch( EEG, triggers, [-.8 1], 'newname', [files(i).name
'epochs'], 'epochinfo', 'yes');
    EEG = eeg_checkset( EEG );
    EEG = pop_rmbase( EEG, [-200    0]);
    EEG = eeg_checkset( EEG );
    %EEG = pop_saveset( EEG,  'filename', strcat(files(i).name,
'_epochs'), 'filepath', savepath);
    [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, CURRENTSET,
'setname', 'epochs');
    EEG = eeg_checkset( EEG );
  
    EEG = pop_saveset( EEG,  'filename', strcat(files(i).name,
'_epochs'), 'filepath', savepath);
    ALLEEG = pop_delset( ALLEEG, [1 2] );
 end
 

Hamish Innes-Brown
Research Assistant, Music and Pitch Project

The Bionic Ear Institute
384-388 Albert Street
East Melbourne, VIC 3002
Tel: +61 3 9667 7529
Fax: +61 3 6997 7518


 

________________________________

From: eeglablist-bounces at sccn.ucsd.edu
[mailto:eeglablist-bounces at sccn.ucsd.edu] On Behalf Of Andrew Hill
Sent: Thursday, 25 June 2009 5:50 PM
To: eeglablist
Subject: Re: [Eeglablist] script example, to extract epochs?


several people have suggested solutions for this - thanks to everyone!
i'm still having issues understanding a few things in EEGLab scripting,
and especially in memory management.  

here is my script:



 

for S = [108 109];
    eeglab
    Cond =[ 'LVF_ConTarg_AllCue'; 'LVF_IncTarg_AllCue';
'RVF_ConTarg_AllCue'; 'RVF_IncTarg_AllCue' ];
    trigs=[110 111 112 113; 120 121 122 123; 210 211 212 213; 220 221
222 223 ]; 

  


   for c = 1:4;


 

    %load a file, for example 108.set, which is not filtered and uses
common vertex reference.  
    EEG = pop_loadset( 'filename', [int2str(S),'.set'], 'filepath',
'/Users/andrew/Documents/Research/DATA/stage/');
    [ALLEEG, EEG, CURRENTSET] = eeg_store( ALLEEG, EEG, 0 );
    EEG = eeg_checkset( EEG );


 

    % re-reference to common average reference, excluding VEOU and VEOL
    EEG = pop_reref( EEG, [], 'refstate',0, 'exclude',[65 66] )

    


    % lookup Channel Locations
    EEG=pop_chanedit(EEG,  'lookup',
'/Users/andrew/Documents/Research/eeglab2008October01_beta/plugins/dipfi
t2.2/standard_BESA/standard-10-5-cap385.elp');

    


    % EXTRACT EPOCHS, for trigs relevant to Cond
    EEG = pop_selectevent( EEG, 'event',trigs(c,:) , 'deleteepochs',
'on');
    [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1, 'setname',
Cond(c,:), 'savenew', [int2str(S),'_AVGREREF_',Cond(c,:)], 'overwrite',
'on', 'gui', 'off'); 

        

    %baseline filter using pre-stimulus interval.  
    %NOT working ->"pop_rmbase(): Wrong point range"
    %EEG = pop_rmbase( EEG, [-1000  0]);

    


    %maybe CLEAR some RAM? NOT working.
    %ALLEEG = pop_delset( ALLEEG, [1] );
    %CURRENTSET = pop_delset()
    end;
end;

so some strangeness:

1) when i save a new .set named per the S(ubject) and Cond(ition), the
'deleteepochs', 'on'doesn't seem to work - the file contains ALL the
epochs, not just 'trigs' ones specified./


2) the pop_rmbase syntax seems to be correct, from my eegh, but when put
in a script it throws "pop_rmbase(): Wrong point range" . and including
'timerange' doesn't help.


3) the biggest problem is this script the second time around the loop,
e.g. it only produces files for the first condition, first subject.


108_AVGREREF_LVF_ConTarg_AllCue.set
108_AVGREREF_LVF_ConTarg_AllCue.dat

and then fails with out of memory errors:
??? Error using ==> ctranspose 
Out of memory. Type HELP MEMORY for your options.

i tried ALLEEG = pop_delset( ALLEEG, [1] ); to clear memory before
running through the Condition loop a 2nd time, but this doesn't work.
what am i doing wrong? is there any better way to clear the memory
before the next loop through?


thanks,
andrew

On Jun 18, 2009, at 4:56 PM, Andrew Hill wrote:




	does anyone have a simple example script, to open a .set file
and
	

	extract a series of epochs by event types into different files?