[FieldTrip] Problems detecting Artifacts in Neuroscan CNT file

Omoniyi Segun omoniyi_s at yahoo.com
Wed Oct 12 19:11:35 CEST 2011


Hi Jan-mathijs,

Did you get a chance to look at the problem described about neuroscan CNT file.

Thanks

Omoniyi Segun  



________________________________
From: Omoniyi Segun <omoniyi_s at yahoo.com>
To: jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>
Sent: Wednesday, October 5, 2011 10:46 AM
Subject: Re: [FieldTrip] Problems detecting Artifacts in Neuroscan EEG file


Thanks for your response.

I am passing a 'subject' structure which contains the file location and file name to the do_reject_artifacts function which i wrote. Inside the function i have inserted the code I got from the tutorial.

The structure is created in a do_preprocess function, i read all the files in a directory structure and create the subject stucture in this function.

The files are Neuroscan .cnt files


Thanks for your help

Omoniyi Segun



snippet from : do_preprocess

        clear subject;
        if ( reply == 'Y' || reply == 'y')
            %token = strtok(subjectdata.filename{i}, '.');
            token = strtok(files(i).name, '.');
            subject.datafile = [subjectdata.datadir filesep subjectdata.taskdir filesep subjectdata.subjectdir filesep files(i).name];
            subject.datafilename = token;
            subject.datafiledir = [subjectdata.datadir filesep subjectdata.taskdir filesep subjectdata.subjectdir];
            subject.artifactdir = subjectdata.artifactdir;


snippet from : do_reject_artifacts

cfg.dataset            = 'subject.datafile;       % name of EEG dataset  
cfg.trialdef.eventtype      = 'trigger';
cfg.trialdef.prestim        = 1;
cfg.trialdef.poststim       = 2;
cfg.trialdef.eventvalue     = [1 2];                                    
cfg = ft_definetrial(cfg);            
data= ft_preprocessing(cfg)
trl = cfg.trl;


%
 jump
cfg                    = [];
cfg.trl = trl;
cfg.padding = 0;


cfg.datafile   = subject.datafile;
cfg.headerfile = subject.datafile;
cfg.continuous = 'yes';

cfg.memory = 'low';

% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel    = 'EEG';
cfg.artfctdef.zvalue.cutoff     = 20;
cfg.artfctdef.zvalue.trlpadding = 0.5*cfg.padding;
cfg.artfctdef.zvalue.artpadding = 0.5*cfg.padding;
cfg.artfctdef.zvalue.fltpadding = 0;
 
% algorithmic parameters
cfg.artfctdef.zvalue.cumulative    = 'yes';
cfg.artfctdef.zvalue.medianfilter  = 'yes';
cfg.artfctdef.zvalue.medianfiltord = 9;
cfg.artfctdef.zvalue.absdiff       = 'yes';
 
% make the process
 interactive
cfg.artfctdef.zvalue.interactive   = 'yes';
 
[cfg, artifact_jump] = ft_artifact_zvalue(cfg,data);




________________________________
From: jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
To: Omoniyi Segun <omoniyi_s at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>
Sent: Tuesday, October 4, 2011 8:15 AM
Subject: Re: [FieldTrip] Problems detecting Artifacts in Neuroscan EEG file


Hi Omoniyi,

What kind of data are you passing to the function? 

BW,

JM




On Oct 3, 2011, at 4:49 PM, Omoniyi Segun wrote:

Hi,
>
>
>I am new to fieldtrip and have been struggling with it for the past four weeks. 
>
>
>
>I am trying to do artifact detection using the Automatic Artifact detection tutorial on the Site. The first issue I am having is when i set % make the process interactive cfg.artfctdef.zvalue.interactive = 'yes';
>I see nothing in the figure that is plotted. I see the data plotted when i use the sample data provided but not when i use my Neuroscan EEG data.
>
>
>Secondly when i click on stop I get the error pasted below.
>
>
>
>
>
>??? Reference to non-existent field 'dimord'.
>
>Error in ==> dimlength at 74
>      elseif strcmp(data.(fld), 'rpt_pos')
>
>Error in ==> fixsampleinfo at 31
>  ntrial = dimlength(data, 'rpt');
>
>Error in ==> ft_checkdata at 579
>  data = fixsampleinfo(data);
>
>Error in ==> ft_rejectartifact at 203
>  data = ft_checkdata(data, 'hassampleinfo', 'yes');
>
>Error in ==> do_reject_artifacts at 70
>data_no_artifact_jump = ft_rejectartifact(cfg,artifact_jump);
>
>Error in ==> do_preprocess at
 45
>                do_reject_artifacts(subject);
>
>
>I am comfortable making changes to the code and would like some pointers in the right direction. I am not sure if this is an issue with Neuroscan data.
>
>
>Thanks
>
>
>Omoniyi Segun
>
>_______________________________________________
>fieldtrip mailing list
>fieldtrip at donders.ru.nl
>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 
Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793 
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