[FieldTrip] segmenting after ICA on continuous data

[Giuseppe Spinelli]

Hi Julian,
got the point! Now it works.

thanks for the fast reply,

Giuseppe

2016-02-04 17:32 GMT+01:00 Julian Keil <julian.keil at gmail.com>:

> Dear Giuseppe,
>
> in your trial-definition step you state:
>
> cfg = [];
> cfg.continuous = 'no';
> cfg.trailfun = 'ft_trialfun_general';
> cfg.trialdef.eventtype = 'stimtype';
> cfg.trialdef.eventvalue = 8
> cfg.trialdef.prestim = 1;
> cfg.trialdef.poststim = 4;
> cfg = ft_definetrial(data_clean);
> segmented = ft_preprocessing(cfg, data_clean);
>
> So, in your call to ft_definetrial, you are not using your cfg-structure.
> Instead, you overwrite your cfg-structure with the output of the
> (incorrectly called) ft_definetrial.
>
> Here's what you could do instead:
> Use your cfg from above with cfg.dataset = subj; in your call to
> ft_definetrial (e.g. cfg = ft_definetrial(cfg)).
> This gives you the cfg.trl-field with your trial definition.
> In the next step, you could use ft_redefinetrial to actually split up your
> (already cleaned) data.
>
> Check this tutorial for more info:
> http://www.fieldtriptoolbox.org/tutorial/continuous
>
> Good luck,
>
> Julian
>
>
> ********************
> *Dr. Julian Keil*
>
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum A007
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
>
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 04.02.2016 um 17:13 schrieb Giuseppe Spinelli:
>
> Dear Fieldtrippers
>
> I am analyzing a .cnt EEG dataset from a Neuroscan amplifier with an
> hardware bandpass filter of 0.05-200 Hz.
> I am having some troubles with segmentation after performing ICA on
> continuous the continuous EEG trace.
>
> Here you find the pipeline I used:
>
> %% reading the dataset:
> subj = 'C:\data\S01.cnt';
> cfg = [];
> cfg.headerfile =  subj;
> cfg.datafile = subj;
> cfg.continuous = 'yes';
> data_cont = ft_preprocessing(cfg);
>
> %% running ICA and cleaning data
> cfg = [];
> cfg.method = 'runica';
> comp = componentanalysis(cfg, data_cont);
>
> cfg = [];
> cfg.component = [1:62];
> cfg.layout = 'C:\data\mylayout1010.lay';
> cfg.comment = 'no';
> ft_topoplotIC(cfg, comp);
>
> cfg          = [];
> cfg.channel  = [1 3 8];
> cfg.viewmode = 'component';
> cfg.layout = 'C:\data\mylayout1010.lay';
> ft_databrowser(cfg, comp);
>
> cfg           = [];
> cfg.component = [1 3];
> data_clean    = ft_rejectcomponent(cfg, comp, data_cont);
>
> Now, in order to segment data I did:
>
> cfg = [];
> cfg.continuous = 'no';
> cfg.trailfun = 'ft_trialfun_general';
> cfg.trialdef.eventtype = 'stimtype';
> cfg.trialdef.eventvalue = 8
> cfg.trialdef.prestim = 1;
> cfg.trialdef.poststim = 4;
> cfg = ft_definetrial(data_clean);
> segmented = ft_preprocessing(cfg, data_clean);
>
> but, the Command Window retured me with the following error:
>
> Reference to non-existent field 'headerfile'.
>
> Error in ft_trialfun_general (line 78)
> hdr = ft_read_header(cfg.headerfile, 'headerformat', cfg.headerformat);
>
> Error in ft_definetrial (line 174)
>     [trl, event] = feval(cfg.trialfun, cfg);
>
>
> I cannot get why both the headerfile and the dataset file are needed to be
> specified again.
> Could someone help me to figure it out?
>
> Many thanks in advance,
>
> Giuseppe Spinelli
>
> Ph.D. student in Cognitive Social and Affective Neuroscience
>
> Department of Psychology, Sapienza University of Rome
> via dei Marsi 78, 00185 - Rome
> Phone/Fax: +39 06-49917635
>
> IRCCS Fondazione Santa Lucia
> via Ardeatina 306, 00179 - Rome
> Phone: +39 06 5150 1108
>
> @: giuseppe.spinelli at uniroma1.it
> http://agliotilab.org/
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-- 
Giuseppe Spinelli

Ph.D. student in Cognitive Social and Affective Neuroscience

Department of Psychology, Sapienza University of Rome
via dei Marsi 78, 00185 - Rome
Phone/Fax: +39 06-49917635

IRCCS Fondazione Santa Lucia
via Ardeatina 306, 00179 - Rome
Phone: +39 06 5150 1108

@: giuseppe.spinelli at uniroma1.it
http://agliotilab.org/
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