[FieldTrip] fieldtrip question - help needed

s.rombetto at cib.na.cnr.it s.rombetto at cib.na.cnr.it
Fri Jan 14 11:40:09 CET 2011


thanks
that's right.
But we also fabricate squids, so the broken channels can change.
  So I was looking for a temporary solution.

best regards
Sara

> Cara Sara,
>
> OK. Indeed, if you have run ft_rejectvisual and removed some channels,
> these are missing from your actual data. The original data.grad should
> however still contain the labels of all channels, and you can use
> grad.label as 'LABEL275', provided the order of the remaining channels
> did not change. Alternatively, you could define cfg.keepchannel =
> 'nan', before calling ft_rejectvisual. The noisy channels will then
> still be 'present' in your data (but set to NaN). I believe that this
> would take away the need to do the first part of the script.
>
> Best
>
> JM
>
> PS: please note that it is not optimal to do source reconstruction
> after replacing noisy channels with an average of their neighbours. At
> least you need to take this into account in the creation of the
> leadfields.
>
>
> On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote:
>
>> Hello
>> yes I'm referring to the example script 'fixing a missing sensor'.   
>> Even if you consider the structure grad, you also load LABEL275.mat  
>>  and GRAD275.mat, that is the layout in someway.
>>
>> What I do is to process my data: I define trials and preprocess   
>> them. Then I use ft_rejectvisual to remove artifacts and noisy   
>> channels.
>> After this my data are ok, but I have some missing channels.
>> In order to solve the inverse problem, I'm using a software that   
>> needs all the channels....and this is the reason why I'm trying to   
>> "fix the missing sensor".
>>
>> Sara
>>
>>> Cara Sara,
>>>
>>> I am not sure whether I totally understand your question. Are you
>>> referring to the example script 'fixing a missing sensor'?
>>> When I look at it on our (renewed) wiki (still brings tears to my
>>> eyes), I don't see any mention of a layout.
>>>
>>> I agree with you that the example however can be made a bit more clear.
>>> This is my take on it, starting from the back of the pipeline:
>>>
>>> The 'fixing' algorithm replaces a 'dead' channel with the average
>>> signal recorded at its neighbours. In the current implementation, the
>>> description of the sensors and the data (=the grad-structure and the
>>> data.trial) which go into ft_channelrepair need to contain a full
>>> description of the sensor-array, including the faulty one. In other
>>> words, if your sensor array has 10 sensors, one of which you want to
>>> have repaired, the input to ft_channelrepair needs a data-structure
>>> containing data from the spatial location of those 10 sensors (this is
>>> in data.grad, and needed to determine which channels are the
>>> neighbours). For consistency, the time course of the faulty channel
>>> also needs to be there. The actual time courses of the faulty channel
>>> will not be used, and these can take any value. Depending on the
>>> hardware and recording protocol, a faulty channel is either present or
>>> not in the data. In the example script, the faulty channel was not even
>>> recorded, and this is the reason for the first part of the script: the
>>> creation of a dummy channel, initialized with 0's in order to make
>>> ft_channelrepair work. If, however, your dataset actually contains data
>>> on the faulty channel (which may look very noisy), you can skip the
>>> first part of the script, and directly go to the second part.
>>>
>>> Best wishes,
>>>
>>> Jan-Mathijs
>>>
>>>
>>> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote:
>>>
>>>> Hello
>>>> can anybody spend some more words on the chapter "Fixing a   
>>>> missing sensor"?
>>>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I
>>>> cannot understand how to use it. I've several troubles when I've to
>>>> declare the layout, since I don't have a layout file, but I construct
>>>> that starting from grad...
>>>> Do you have any hint for me?
>>>>
>>>> Sara Rombetto
>>>>
>>>>
>>>> -------------------------------------------
>>>> * Dott.ssa Sara Rombetto                   *
>>>> * Istituto di Cibernetica "E. Caianiello"  *
>>>> * Via Campi Flegrei, 34                    *
>>>> * 80078 Pozzuoli (NA)                      *
>>>> * Italy                                    *
>>>> * tel +390818675054                        *
>>>> * fax +390818675326                        *
>>>> -------------------------------------------
>>>>
>>>> ----------------------------------------------------------------
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>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>> Dr. J.M. (Jan-Mathijs) Schoffelen
>>> Donders Institute for Brain, Cognition and Behaviour,
>>> Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>> J.Schoffelen at donders.ru.nl
>>> Telephone: 0031-24-3614793
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> -------------------------------------------
>> * Dott.ssa Sara Rombetto                   *
>> * Istituto di Cibernetica "E. Caianiello"  *
>> * Via Campi Flegrei, 34                    *
>> * 80078 Pozzuoli (NA)                      *
>> * Italy                                    *
>> * tel +390818675054                        *
>> * fax +390818675326                        *
>> -------------------------------------------
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



-------------------------------------------
* Dott.ssa Sara Rombetto                   *
* Istituto di Cibernetica "E. Caianiello"  *
* Via Campi Flegrei, 34                    *
* 80078 Pozzuoli (NA)                      *
* Italy                                    *
* tel +390818675054                        *
* fax +390818675326                        *
-------------------------------------------

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