[FieldTrip] channelrepair issue
Jim Li
megjim1 at gmail.com
Fri Jul 8 01:38:46 CEST 2011
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
>>
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>
> -----------------------
> 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
>
>
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