[FieldTrip] channelrepair issue

[Jim Li]

Thank you very much for confirming the problem, Don, I appreciate it, :)

Jim

On Thu, Jul 7, 2011 at 4:30 PM, Rojas, Don <Don.Rojas at ucdenver.edu> wrote:

> Jim,
>
> All I can do is confirm that this issue exists for our 4D data as well,
> although we don't use the ft_channelrepair function. The same 4 quite
> distant channels (one had been deleted in the dataset I had handy) were
> chosen for repair when I ran this on one of our datasets (also a 248 channel
> 4D system). I agree the choice doesn't make any sense given the 3 cm
> distance you define. A quick look at the critical calculation in
> ft_channelrepair, line 109 distance = ... is correct given the inputs. So I
> wonder if the issue is with the actual channel indices used rather than the
> calculation, but I don't have time to track that down. All I can say is that
> for the distance you specify, channels A235, A216, A199, A215 would be much
> closer to A234 than those that are selected via the channel repair function.
> Channel A8 is in fact nearly 21 cm away from channel A234 in the array,
> based on examination of the data read in from Eugene Kronberg's pdf4D matlab
> object code, which I think was originally the basis for the FieldTrip 4D
> reader function.
>
> Best,
>
> Don Rojas
>
>
>    On Jul 7, 2011, at 1:26 PM, Jim Li wrote:
>
>   Dear Fieldtrip developer,
>
> Can anybody help me with this channel-repair issue I've been having? I can
> provide the raw data if you need. I really want to solve the problem, you
> know.
>
> Thanks a lot,
>
> Jim
>
> On Thu, Jul 7, 2011 at 2:22 PM, Jim Li <megjim1 at gmail.com> wrote:
>
>> 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
>>
> _______________________________________________
>
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>  -----------------------
> Don Rojas, Ph.D.
> Associate Professor of Psychiatry
> U. of Colorado Denver Anschutz Medical Campus
> Director, UCD Magnetoencephalography Lab
> 13001 E. 17th Pl F546
> Aurora, CO 80045
> 303-724-4994
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110707/4a7bd588/attachment-0002.html>