[FieldTrip] ft_channelrepair shows no effect at all

[KatrinH Heimann]

Dear Eelke,

ok, so i installed an older version of matlab (which also solved some other
problems with fieldtrip) and now it works. However I am running into
another problem with it. Maybe you can help too:
If I try to run the ICA after the bad channel replacement it takes hours
and wchange just does not get lower. In my naive thinking I thought that
might be due to the fact that the replaced channels are recognized as
interpolations of the others??? But what could I do otherwise?: I thought
about doing the bcr later, but that means that my ica suffers from all the
electrode jumps from my bad channels. or I just exclude them from the ica -
but how to proceed then: apply the reject component function on the data
without the channels and then replace them? sorry, I am just a bit lost.
The weirdest thing is: if I replace the channels with the help of another
software before even processing the data, the ica works perfectly later in
fieldtrip. WHY????
Would be wonderful if you could give me another hand... Thanks so much in
advance!!!
Katrin


2014-08-18 10:18 GMT+02:00 Eelke Spaak <eelke.spaak at donders.ru.nl>:

> Dear Katrin,
>
> When I look at the data you've shown me, in fact I do see an effect of
> ft_channelrepair. I run your code:
>
> load ('ERP_Francesca17obs90_clean.mat')
>
> %% Preparing neighbours for channel repair
>
> cfg_neighb = [];
> cfg_neighb.feedback = 'yes';
> cfg_neighb.method = 'triangulation';
> cfg_neighb.layout = 'GSN-HydroCel-129.sfp';
> neighbours = ft_prepare_neighbours(cfg_neighb, obs90_data_clean2);
>
> % Interpolate and put into new data structure
> cfg = [];
> cfg.badchannel = {'E49', 'E68'};
> cfg.layout = 'GSN-HydroCel-129.sfp';
> cfg.method = 'nearest';
> cfg.neighbours = neighbours;
> obs90_data_channelrepaired = ft_channelrepair(cfg,obs90_data_clean2);
>
> followed by:
>
> dat1=obs90_data_clean2;
> dat2=obs90_data_channelrepaired;
>
> x=dat1.trial{1}(68,:); % 68 is channel index of E68
> y=dat2.trial{1}(68,:);
> plot(x);hold on;plot(y,'r');
>
> x=dat1.trial{1}(49,:);
> y=dat2.trial{1}(49,:);
> figure;
> plot(x);hold on;plot(y,'r')
>
> and the two figures that come up are shown in the attachments. The
> original (blue) and channel-repaired (red) traces are clearly
> different. These plots are for trial 1, but the same result holds when
> I plot a different trial.
>
> Does it work on your end too now?
>
> Best,
> Eelke
>
> On 14 August 2014 08:57, Eelke Spaak <eelke.spaak at donders.ru.nl> wrote:
> > OK just checking :) In that case, could you post a small snippet of
> > data and the actual cfg you used (including which channels to repair)
> > on e.g. dropbox or so? Then I can have a look.
> >
> > Best,
> > Eelke
> >
> > On 13 August 2014 22:12, KatrinH Heimann <katrinheimann at gmail.com>
> wrote:
> >> Dear Eelke, yes, sure, sorry, I did that. No effect.
> >>
> >>
> >> 2014-08-13 21:55 GMT+02:00 Eelke Spaak <eelke.spaak at donders.ru.nl>:
> >>
> >>> Dear Katrin,
> >>>
> >>> Have you tried putting the labels of the channels you want interpolated
> >>> into the cfg.badchannel array?
> >>>
> >>> Best,
> >>> Eelke
> >>>
> >>> Op 13 aug. 2014 19:24 schreef "KatrinH Heimann" <
> katrinheimann at gmail.com>:
> >>>>
> >>>> Dear all. I am trying to replace bad channels.
> >>>> This is my code (very basic I think):%% Preparing neighbours for
> channel
> >>>> repair
> >>>>
> >>>>
> >>>>
> >>>> cfg_neighb          = [];
> >>>>
> >>>> cfg_neighb.feedback = 'yes';
> >>>>
> >>>> cfg_neighb.method   = 'triangulation';
> >>>>
> >>>> cfg_neighb.layout   = 'GSN-HydroCel-129.sfp';
> >>>>
> >>>> neighbours          = ft_prepare_neighbours(cfg_neighb, obs_data);
> >>>>
> >>>>
> >>>>
> >>>> % Interpolate and put into new data structure
> >>>>
> >>>>  cfg                      = [];
> >>>>
> >>>>  cfg.badchannel           = {};
> >>>>
> >>>>  cfg.layout               = 'GSN-HydroCel-129.sfp';
> >>>>
> >>>>  cfg.method               = 'nearest';
> >>>>
> >>>>  cfg.neighbours           = neighbours;
> >>>>
> >>>>  obs_data_channelrepaired       = ft_channelrepair(cfg,obs_data)
> >>>>
> >>>>
> >>>> I do not get any error but fieldtrip even tells me that the
> interpolation
> >>>> worked. However I do not see ANY trace of it in my data when
> inspecting it
> >>>> afterwards. I also tried to change the method (to average) - no
> change.
> >>>> Anybody who can help me with that?
> >>>> Thanks a million
> >>>> Katrin
> >>>>
> >>>>
> >>>>
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> >>>
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> >>
> >>
> >>
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