[FieldTrip] 回复： Re: 回复： Re: How to plot ERP waveforms
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Wed Jan 8 12:52:38 CET 2014
Hi Lin Cai,
you have to solve it yourself by checking your data and cfg. I cannot
help with that.
Best,
Jörn
On 1/8/2014 12:46 PM, 蔡林 wrote:
> I can not understand what you mean. Please give me some detail infomation about how to solve this problem.
> ----- 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 19:12:31 +0800 (CST)
> 主题: Re: [FieldTrip] 回复： Re: How to plot ERP waveforms
>
> Hi Lin Cai,
>
> check whether your trl-matrix (matrices) makes sense. The error means
> that e.g. according to the sampleinfo there should be a different number
> of trials than your data contains or stuff the like. So, just at it
> says, some inconsistency between the sampleinfo field (which is part of
> the trl-matrix) and your data.
>
> Best,
> Jörn
>
> On 1/7/2014 11:50 AM, 蔡林 wrote:
>> 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);
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
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:
E-Mail: jm.horschig at donders.ru.nl
Tel: +31-(0)24-36-68493
Web: http://www.ru.nl/donders
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
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