[FieldTrip] 回复： Re: How to plot ERP waveforms
蔡林
bertram0611 at pku.edu.cn
Tue Jan 7 11:50:44 CET 2014
Hi,
I can run my codes according to what you told me. And I saw four conditions in a figure. Thanks for your help.
But there are still something wrong with my codes. Because I saw warnings in the Command Window in Matlab.
As follows:
Warning: the trial definition in the configuration is inconsistent with the actual data
> In utilities\private\warning_once at 158
In utilities\private\fixsampleinfo at 68
In ft_datatype_raw at 154
In ft_checkdata at 298
In ft_preprocessing at 240
In outputplot at 5
Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a
continuous recording
> In utilities\private\warning_once at 158
In utilities\private\fixsampleinfo at 79
In ft_datatype_raw at 154
In ft_checkdata at 298
In ft_preprocessing at 240
In outputplot at 5
preprocessing
preprocessing trial 1 from 1
the call to "ft_preprocessing" took 0 seconds
********
Why the data were preprocessed from trial 1 to 1????
Am I right in the whole codes?
Thank you in advance.
Lin Cai
----- 原始邮件 -----
发件人: Jörn M. Horschig <jm.horschig at donders.ru.nl>
收件人: FieldTrip discussion list <fieldtrip at science.ru.nl>
已发送邮件: Tue, 07 Jan 2014 17:02:46 +0800 (CST)
主题: Re: [FieldTrip] How to plot ERP waveforms
Hi,
tricky problem, and a very nasty one, but it's a simple one in the end ;)
Once you call ft_definetrial you get back a cfg with a .trl matrix. Upon
the next call to ft_definetrial, FieldTrip checks for the presence of
cfg.trl, and if so returns immediately (because ft_definetrial has been
called before). Thus, in the beginning when you compute data_14,
data_24, etc, they will all be based on the same trl. Therefore, the
same data will be computed and all four plots will overlap.
You need to change the name of the output argument for each
ft_definetrial call to be unique to resolve this, something like:
cfg_14 = ft_definetrial(cfg);
cfg_14.channel = {'all'};
data_14 = ft_preprocessing(cfg_14);
cfg.trialdef.eventvalue = [24]; %markers
cfg_24 = ft_definetrial(cfg);
cfg_24.channel = {'all'};
data_24 = ft_preprocessing(cfg_24);
Best,
Jörn
On 1/7/2014 9:42 AM, 蔡林 wrote:
> Dear fieldtripers,
>
> I am coming across a problem about plotting.I have four conditions in my experiment, but why did the figure have only one conditon? Please help me if you find something wrong with my codes. My codes are as follows:
>
>
> %%preprocessing 40 subjects
> nsubjects = [1:40];
> for i=1:length (nsubjects)
> j = nsubjects(i);
> cfg = [];
> cfg.dataset = sprintf('s%d-epoch-bsline.eeg', j);
> cfg.trialdef.eventtype = 'trial';
> cfg.trialdef.eventvalue = [14]; %markers
> cfg = ft_definetrial(cfg);
> cfg.channel = {'all'};
> data_14 = ft_preprocessing(cfg);
>
> cfg.trialdef.eventvalue = [24]; %markers
> cfg = ft_definetrial(cfg);
> cfg.channel = {'all'};
> data_24 = ft_preprocessing(cfg);
>
> cfg.trialdef.eventvalue = [34]; %markers
> cfg = ft_definetrial(cfg);
> cfg.channel = {'all'};
> data_34 = ft_preprocessing(cfg);
>
> cfg.trialdef.eventvalue = [44]; %markers
> cfg = ft_definetrial(cfg);
> cfg.channel = {'all'};
> data_44 = ft_preprocessing(cfg);
>
> outfil = strcat('/EEG/data_s', sprintf('%02d', j));
> save(outfil, 'data_14','data_24','data_34','data_44');
> clear data_14* data_24* data_34* data_44*;
> end
> %% calculate the ERP of each subject
> nsubject = [1:40];
>
> for i=1:length (nsubject)
> j=nsubject(1,i);
> load (sprintf('/EEG/data_s%02d',j));
>
> cfg = [];
> cfg.latency = [-0.2 1.0];
> cfg.covariance = 'no';
> cfg.blcovariance = 'no';
>
> avg_14=ft_timelockanalysis(cfg,data_14);
> avg_24=ft_timelockanalysis(cfg,data_24);
> avg_34=ft_timelockanalysis(cfg,data_34);
> avg_44=ft_timelockanalysis(cfg,data_44);
>
> cfg = [];
> cfg.baseline = [-0.2 0];
> cfg.baselinetype = 'absolute';
> base_14= ft_timelockbaseline(cfg, avg_14);
> base_24= ft_timelockbaseline(cfg, avg_24);
> base_34= ft_timelockbaseline(cfg, avg_34);
> base_44= ft_timelockbaseline(cfg, avg_44);
>
> outfil = strcat('/EEG/baseERP_resp_s', sprintf('%02d', j));
> save(outfil, 'base_14', 'base_24', 'base_34', 'base_44','avg_14', 'avg_24', 'avg_34','avg_44');
> clear avg* data*;
> end
> %% calculate the grand average of the 40 subjects
> %%grand average
> cfg = [];
> nsubject = [1:40];
>
> for i=1:length (nsubject)
> j=nsubject(1,i);
> load(sprintf('/EEG/baseERP_resp_s%02d',j));
>
> sub_14(i).ERP= avg_14;
> sub_24(i).ERP= avg_24;
> sub_34(i).ERP= avg_34;
> sub_44(i).ERP= avg_44;
> clear avg*
> end
>
> grandavg_14 = ft_timelockgrandaverage(cfg, sub_14(:).ERP); %C
> grandavg_24 = ft_timelockgrandaverage(cfg, sub_24(:).ERP); %Refer
> grandavg_34 = ft_timelockgrandaverage(cfg, sub_34(:).ERP); %Semantic
> grandavg_44 = ft_timelockgrandaverage(cfg, sub_44(:).ERP); %Double
>
> outfil = strcat('/EEG/n40_grandavgERP_resp');
> save(outfil, 'grandavg_14', 'grandavg_24', 'grandavg_34', 'grandavg_44');
> %%plotting
> load /EEG/n40_grandavgERP_resp;
>
> cfg = [];
> cfg.layout = 'EEG1010.lay';
> cfg.xlim = [-0.2 1.0];
>
> cfg.baseline = 'no';
> cfg.interactive = 'no';
> cfg.showlabels = 'yes';
> cfg.colorbar = 'yes';
>
> figure;
> ft_multiplotER(cfg,grandavg_14, grandavg_24, grandavg_34, grandavg_44);
>
>
>
>
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--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
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Visiting address:
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--
Lin Cai
Department of Psychology, Peking University, Beijing 100871, P.R.China
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