[FieldTrip] using ft_definetrial
Nikola Valchev
nikola.valchev.umcg at gmail.com
Fri Jul 17 15:48:44 CEST 2015
Dear Stan,
Thank you very much for your help. I think I found where the problem is. The
format of my data is EEProbe and apparently fieldtrip doesnt red it
correctly. I managed to import it in eeglab and then use the magic function
eeglab2fieldtrip.
Best
Nikola
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Pelt, S. van (Stan)
Sent: 14 July 2015 14:53
To: FieldTrip discussion list
Subject: Re: [FieldTrip] using ft_definetrial
Hi Nikola,
I have no experience with EEG data myself. But If I understand correctly,
the relevant trigger information is in your .trg-file.
So, if you can define variable triggers as below, it should be relatively
straigthforward:
triggers= [ 0.000000 0 0
20.568359 2490491 1
23.787109 2879419 9
28.597656 3460687 1
33.056641 3999475 3
45.923828 5554243 1
...]
It seems that you have 118*1024 samples (segments) per second, is that
correct? And your EEG-data is time-labeled in segments, not seconds?
Now, your trigger values of interest (1) are in column 3, not in 2, that is
the crucial bit probably:
u1=find(ismember(triggers(:,3),[1]));
And then you can do
trl= [triggers(u1,2)-.2*1024 triggers(u1,2)+6*1024
repmat(-.2*1024,numel(u1),1)];
You might want to change 0.2 into e.g. 0.25, since otherwise you might end
up with non-integer values.
To get rid of your last error, make sure that there are no negative sample
numbers in your cfg.trl (since theres no data befor sample nr 0).
Best,
Stan
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Nikola Valchev
Sent: dinsdag 14 juli 2015 14:36
To: 'FieldTrip discussion list'
Subject: Re: [FieldTrip] using ft_definetrial
Hi Pelt,
Thanks a lot for the help. Somehow I forgot that I can specify my own trl
matrix manually...
(Im sorry for the long email but I try to be as clear as possible so that
it takes less time.)
However, there is still something wrong which I dont understand. What I do
is to use ft_read_event to read all the triggers and events from the cnt
file. What I get is the event structure with the fileds
type
sample
value
offset
duration
I presume that these are read from the trg file (i.e. s14_CI_1.trg which is
associated with the s14_CI_1.cnt).
Inside that file I have:
0.000000 0 0
20.568359 2490491 1
23.787109 2879419 9
28.597656 3460687 1
33.056641 3999475 3
45.923828 5554243 1
...
First column should be the times, second the segment and the third the
trigger. I use your commands to create the matrix:
u1=find(ismember(triggers(:,2),[1]));
trl= [triggers(u1,2)-.2*1024 triggers(u1,2)+6*1024
repmat(-.2*1024,numel(u1),1)];
And at the end I get a matrix:
1.0e+003 *
-0.2038 6.1450 -0.2048
-0.2038 6.1450 -0.2048
-0.2038 6.1450 -0.2048
-0.2038 6.1450 -0.2048
...
Then I attempt to preprocess again:
cfg=[];
cfg.dataset='C:\eeg_anita\data\S14\s14_CI_1.cnt';
cfg.headerfile='C:\eeg_anita\data\S14\s14_CI_1.cnt';
cfg.trl=trl;
cfg_test=ft_preprocessing(cfg);
and I get an error:
??? Error using ==> ft_read_data at 206
cannot read data before the begin of the file
Error in ==> ft_preprocessing at 563
dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
begsample, 'endsample', endsample, 'chanindx', rawindx,
'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
cfg.dataformat)
Nikola
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Pelt, S. van (Stan)
Sent: 14 July 2015 09:25
To: FieldTrip discussion list
Subject: Re: [FieldTrip] using ft_definetrial
Hi Nikola,
You might also try a workaround:
% read the events from the data
event = ft_read_event('C:\eeg_anita\data\S14\s14_CI_1.cnt');
% search for "trigger" events
triggers=[];
for i=1:size(event,1)
a=find(strcmp(event(i).type,'trigger')==1);
if a>0
triggers=[triggers; event(i).value event(i).sample];
end
end
% make cfg.trl: I think this is where things go wrong in your script. You
could check whats in triggers(:,1). Otherwise, whats below should work:
u1=find(ismember(triggers(:,1),[1 3 6 9])); % select your eventvalue(s) of
interest
trl= [triggers(u1,2)-.2*fs triggers(u1,2)+6*fs repmat(-.2*fs,numel(u1),1)];
% 0.2 prestim, 6s post-stim, with fs being your sampling frequency
% next, do preprocessing, with cfg.trl=trl;
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Jörn M. Horschig
Sent: dinsdag 14 juli 2015 8:38
To: 'FieldTrip discussion list'
Subject: Re: [FieldTrip] using ft_definetrial
Hi Nikola,
seems to be a nasty problem. Id start with using event =
ft_read_events(cfg.dataset) and then check up the event-structure on how
they are defined there. ft_trialfun_general is literally checking that
event-structure, so defining them like they are specified in there might
help.
Best,
Jörn
--
Jörn M. Horschig, PhD, Software Engineer
<http://www.artinis.com/> Artinis Medical Systems | +31 481 350 980
From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Nikola Valchev
Sent: Monday, July 13, 2015 9:51 PM
To: 'FieldTrip discussion list'
Subject: Re: [FieldTrip] using ft_definetrial
Nope. Thats not it. No matter if I declare it as a double or string when I
call the eventtype trigger instead of ? they are not read.
Nikola
From: <mailto:fieldtrip-bounces at science.ru.nl>
fieldtrip-bounces at science.ru.nl [ <mailto:fieldtrip-bounces at science.ru.nl>
mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Pelt, S. van (Stan)
Sent: 13 July 2015 19:30
To: FieldTrip discussion list
Subject: Re: [FieldTrip] using ft_definetrial
What about
cfg.trialdef.eventvalue = 1;
Op 13 jul. 2015, om 18:36 heeft Eelke Spaak <
<mailto:eelke.spaak at donders.ru.nl> eelke.spaak at donders.ru.nl> het volgende
geschreven:
cfg.trialdef.eventvalue = {'1'};
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