[FieldTrip] ft_rejectvisual channel selection
Lozano Soldevilla, D. (Diego)
d.lozanosoldevilla at fcdonders.ru.nl
Tue May 17 09:37:09 CEST 2011
Thanks for your explanation Eelke ;). Now all makes sense.
Diego
----- "Eelke Spaak" <eelke.spaak at donders.ru.nl> wrote:
> From: "Eelke Spaak" <eelke.spaak at donders.ru.nl>
> To: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Sent: Tuesday, 17 May, 2011 9:28:36 AM
> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>
> Hi Diego,
>
> Indeed, it is probably a good idea to check for artifacts before
> performing any resampling. The sample indices that are stored in trl
> (or sampleinfo) matrices, should always correspond to sample indices
> in the *original* dataset (on disk), and do not necessarily have any
> direct relation to sample indices in the data you have in memory.
> Therefore, if you resample the data, the samples in your data in
> memory do not directly correspond to samples in the dataset on disk
> anymore; so therefore trl or sampleinfo fields would not make sense,
> and might even lead to inconsistencies. This is the reason that
> ft_resampledata removes any such fields, if present, from your
> (in-memory) dataset.
>
> We are currently in the process of thinking hard about the trl and
> sampleinfo matrices, and might revise how these are handled in the
> future. In any case, it should become possible (already on our
> todo-list) to use the artifact detection functions on in-data memory
> without explicit sample indices.
>
> But, for now, your solution is the quickest one :)
>
> Best,
> Eelke
>
> 2011/5/17 Lozano Soldevilla, D. (Diego)
> <d.lozanosoldevilla at fcdonders.ru.nl>:
> > Hi Stan,
> >
> > You're right. It seems that my problem lies in the lack of trl
> because I previously resample my data and this last function do not
> creates a new trl with the updated begin and end samples. If I create
> a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs)
> *data.fsample);, I get the same error but not with the original data
> (without resampling). Then I'll use data without resampling to check
> my artifacts.
> >
> > Thanks again,
> >
> > Diego
> >
> >
> >
> > ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
> >
> >> From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> >> To: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> >> Sent: Monday, 16 May, 2011 9:40:11 PM
> >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >>
> >> Hi Diego,
> >>
> >> Hm, sounds odd to me. Is your trial-definition output from
> >> ft_definetrial
> >> correct? So a cfg.trl that is not empty?
> >>
> >> Otherwise, you might try starting with an empty cfg again before
> >> calling
> >> ft_preprocessing?
> >>
> >> cfg=ft_definetrial(cfg);
> >> trials=cfg.trl;
> >>
> >> cfg=[];
> >> cfg.trl=trials;
> >> cfg.dataset = [direc d(rr,1).name];
> >> cfg.channel = {'MEG' 'EEG057' 'EEG058'};
> >> cfg.continuous = 'yes';
> >> etc..
> >> data = ft_preprocessing(cfg);
> >>
> >> That should give you an output with a trial-structure, I'd say.
> >>
> >> Best,
> >> Stan
> >>
> >> -----Original Message-----
> >> From: fieldtrip-bounces at donders.ru.nl
> >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> >> Soldevilla,
> >> D. (Diego)
> >> Sent: Monday, May 16, 2011 4:25 PM
> >> To: Email discussion list for the FieldTrip project
> >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >>
> >> Hi Stan,
> >>
> >> Thanks for your quickly answer. I get this error:
> >>
> >> Warning: the data does not contain a trial definition, assuming
> that
> >> the
> >> trials are consecutive segments of a continuous recording
> >> > In utilities/private/warning_once at 81
> >> In utilities/private/fixtrialdef at 52
> >> In ft_datatype_raw at 91
> >> In ft_checkdata at 161
> >> In ft_databrowser at 120
> >> redrawing with viewmode butterfly
> >> ??? Improper index matrix reference.
> >>
> >> Error in ==> ft_databrowser>redraw_cb at 910
> >> evtsample = [event(:).sample];
> >>
> >> Error in ==> ft_databrowser at 419
> >> redraw_cb(h);
> >>
> >> I don't know why my data have no trial definition when I'm sure
> that
> >> is
> >> epoched... Any ideas?
> >>
> >> Thanks in advance,
> >>
> >> Diego
> >>
> >>
> >>
> >> ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
> >>
> >> > From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> >> > To: "Email discussion list for the FieldTrip project"
> >> <fieldtrip at donders.ru.nl>
> >> > Sent: Monday, 16 May, 2011 4:16:16 PM
> >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >> >
> >> > Hi Diego,
> >> >
> >> > You could try using ft_databrowser instead of ft_rejectvisual
> >> > (followed by
> >> > ft_rejectartifact), so:
> >> >
> >> > cfg = [];
> >> > cfg.continuous = 'no';
> >> > cfg.channel = {'EEG057','EEG058'};
> >> > cfg = ft_databrowser(cfg,data);
> >> >
> >> > I think it should work like this.
> >> >
> >> > Best,
> >> > Stan
> >> >
> >> > -----Original Message-----
> >> > From: fieldtrip-bounces at donders.ru.nl
> >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> >> > Soldevilla,
> >> > D. (Diego)
> >> > Sent: Monday, May 16, 2011 4:00 PM
> >> > To: fieldtrip at donders.ru.nl
> >> > Subject: [FieldTrip] ft_rejectvisual channel selection
> >> >
> >> > Dear Fieldtrippers,
> >> >
> >> > I'm using ft_rejectvisual function to reject visually EOG
> artifacts
> >> > of
> >> > epoched trials. My problem consist that I'm not able to plot
> only
> >> the
> >> > EOG
> >> > channels even when I explicitly select them ignoring the 'MEG'
> >> > channels (I
> >> > get a plot with all channels MEG + EOG).
> >> >
> >> > I directly used rejectvisual_channel (used in line 263
> >> > offt_rejectvisual)
> >> > function selecting the EOG channels but I'm getting again all
> >> > channels.
> >> > Somebody could tell me what I'm doing wrong?
> >> >
> >> > Thanks in advance,
> >> >
> >> > Diego
> >> >
> >> >
> >> >
> >> > PS: Code
> >> >
> >> > %epoching
> >> > cfg = [];
> >> > cfg.dataset = [direc d(rr,1).name];
> >> > cfg.trialdef.eventtype = 'frontpanel trigger';
> >> > cfg.trialdef.eventvalue = 4;
> >> > cfg.trialdef.prestim = 1; % in seconds
> >> > cfg.trialdef.poststim = 4; % in seconds
> >> > cfg.trialdef.epochmoving = 'inbackward';
> >> > cfg.trialdef.pivoteventvalue = 2;% cue stimulus
> >> > cfg.trialdef.jumps = 1;
> >> > cfg.trialfun = 'trialselec';
> >> >
> >> > cfg = ft_definetrial(cfg);
> >> >
> >> > cfg.channel = {'MEG' 'EEG057' 'EEG058'};
> >> > cfg.lpfilter = 'yes';
> >> > cfg.lpfreq = 250;
> >> > cfg.baselinewindow = [-1 0];
> >> > cfg.keeptrials = 'yes';
> >> > cfg.demean = 'yes';
> >> > cfg.continuous = 'yes';
> >> >
> >> > data = ft_preprocessing(cfg);
> >> >
> >> > %..............
> >> >
> >> >
> >> > %visual data rejection
> >> > cfg = [];
> >> > cfg.channel = {'EEG057' 'EEG058'};
> >> > cfg.method = 'channel';
> >> > cfg.keepchannel = 'yes';
> >> > data_c = ft_rejectvisual(cfg,data);
> >> >
> >> >
> >> >
> >> > --
> >> > PhD Student
> >> > Donders Institute for Brain, Cognition and Behaviour
> >> > Centre for Cognitive Neuroimaging
> >> > Trigon, room 0.83
> >> > Kapittelweg 29
> >> > Radboud University Nijmegen
> >> > NL-6500 HB Nijmegen
> >> > The Netherlands
> >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> >> > Tel: +31-(0)24-36-66274
> >> > Web: http://www.neuosc.com/
> >> > _______________________________________________
> >> > fieldtrip mailing list
> >> > fieldtrip at donders.ru.nl
> >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> >> > fieldtrip mailing list
> >> > fieldtrip at donders.ru.nl
> >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>
> >> --
> >> PhD Student
> >> Donders Institute for Brain, Cognition and Behaviour
> >> Centre for Cognitive Neuroimaging
> >> Trigon, room 0.83
> >> Kapittelweg 29
> >> Radboud University Nijmegen
> >> NL-6500 HB Nijmegen
> >> The Netherlands
> >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> >> Tel: +31-(0)24-36-66274
> >> Web: http://www.neuosc.com/
> >>
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
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> >> fieldtrip mailing list
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> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
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> >
>
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--
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Trigon, room 0.83
Kapittelweg 29
Radboud University Nijmegen
NL-6500 HB Nijmegen
The Netherlands
E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
Tel: +31-(0)24-36-66274
Web: http://www.neuosc.com/
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