[FieldTrip] channelrepair issue

[Jim Li]

Hi Odelia,

Yes, I downloaded the latest version of Fieldtrip and tried your suggestion
"cfg.neighbourdist = 0.03",   but it still weirdly uses the far-away
channels like A121 to do the channel-repair for A234 (these two channels are
24.1172cm apart!).  Here is the detail:

---------------------------
cfg                         = [];
cfg.dataset                 = 'e,rfhp0.1Hz';
cfg.trialdef.eventtype      = 'TRIGGER';
cfg.trialdef.eventvalue     = 320;
cfg.trialdef.prestim        = 1;
cfg.trialdef.poststim       = 1;
cfg                         = ft_definetrial(cfg);
cfg.blc                     = 'yes';                              % do
baseline correction with the complete trial
cfg.blcwindow               = [-1 0];
cfg.channel                 = {'MEG'};
raw_DATA                    = ft_preprocessing(cfg);


cfg = [];
cfg.badchannel = {'A234'};
cfg.neighbourdist =  0.03;
[raw_DATA] = ft_channelrepair(cfg, raw_DATA)

---------------------------------------------------------------------

And here is the outcome: -----------------------------

the input is raw data with 248 channels and 201 trials
repairing channel A234
  using neighbour A121
  using neighbour A143
  using neighbour A173
  using neighbour A8
repairing bad channels for trial 1
repairing bad channels for trial 2
repairing bad channels for trial 3
repairing bad channels for trial 4
repairing bad channels for trial 5
repairing bad channels for trial 6
repairing bad channels for trial 7
repairing bad channels for trial 8
repairing bad channels for trial 9
repairing bad channels for trial 10
....

-------------------------

Thank you.

Jim

On Thu, Jun 30, 2011 at 4:04 AM, odelia nakar <odidodi at hotmail.com> wrote:

>  Hi Jim,
>
> Try :
> cfg.neighbourdist = 0.03;
> I found it good for my data. (When you run the function the channels that
> repaired your data is displayed in the command window).
>
> Good luck!
> Odelia.
>
>
>  ------------------------------
> Date: Thu, 30 Jun 2011 01:05:08 -0500
> From: megjim1 at gmail.com
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] channelrepair issue
>
>
> Dear all,
>
> We have 4D's WH3600 MEG system (248 channels) and we found the
> -----------------
> cfg = [];
> cfg.dataset =
> 'e,rfhp0.1Hz'; cfg.trialdef.eventtype = 'TRIGGER';
> cfg.trialdef.eventvalue = 320;
> cfg.trialdef.prestim = 1;
> cfg.trialdef.poststim = 1
> ; cfg = ft_definetrial(cfg);
> cfg.blc =
> 'yes'; cfg.blcwindow = [-1 0];
> cfg.channel = {'MEG'};
> raw_DATA = ft_preprocessing(cfg);
> raw_DATA.grad = ft_convert_units(raw_DATA.grad, 'cm')
>
> cfg = [];
> cfg.badchannel = {'A234'};
> [raw_DATA] = ft_channelrepair(cfg, raw_DATA)
> the input is raw data with 248 channels and 201 trials
> repairing channel A234
>   using neighbour A121
>   using neighbour A143
>   using neighbour A154
>   using neighbour A173
>   using neighbour A224
>   using neighbour A8
>   using neighbour A91
> repairing bad channels for trial 1
> repairing bad channels for trial 2
> repairing bad channels for trial 3
> ...
> ------------------------------------
>
> But channels like A121 and A143 are far away from the bad channel A234. How
> can they be used as neighbours (i.e. within 4cm, the default value for
> cfg.neighbourdist) for this bad channel?
>
> Any suggestions?
>
> Thanks a lot.
>
> Jim
>
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