[FieldTrip] Mismatch between channel label and position in hdr.grad (Neuromag 306 system)

[Hanneke van Dijk]

Hi Jarang,

Thanks for the code!

I'm happy I could help you!

Best,

Hanneke
Op 27 jun. 2012 13:00 schreef "Jarang Hahm" <jarang.hahm at gmail.com> het
volgende:

> Dear Hanneke,
>
>
> Thanks to you, I properly found neighbours. :-)
>
> And I confirmed it by plotting the neighbours. To do this, I modified a
> code 'ft_plotneighbours' for correcting a mismatch between the channel
> position and label.
>
> You also probably need this code, so I have attatched what I modified. :-)
>
>
> Thanks!
>
>
> Best,
>
>
> Jarang Hahm
>
>
> On Mon, Jun 25, 2012 at 6:01 PM, Hanneke van Dijk <
> Hanneke.vanDijk at med.uni-duesseldorf.de> wrote:
>
>> Dear Jarang,
>>
>> Coincidentily I have been working on the same problem a few weeks ago.
>>
>>  First of all you should take care that you repair a horizontal
>> gradiometer with neighbouring horizontal gradiometers and vertical ones
>> with vertical ones. This is not built into fieldtrip yet.
>>
>> I have have made a partial fix, which works with the 'layout' option but
>> not with the 'grad' method. I have attached the function I addapted from
>> Fieldtrip, and the layout files that seperatly name the different
>> gradiometers (made by Elisabeth May ;-) )
>>
>> I hope it somehow helps you!
>>
>> Best regards,
>>
>> Hanneke van Dijk
>>
>> ________________________________________________________________
>>
>>
>> Hanneke van Dijk, PhD
>>
>>
>> http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html
>>
>> Institute for Clinical Neuroscience,
>>
>> Heinrich Heine Universität Düsseldorf, Germany
>>
>> Hanneke.vanDijk at med.uni-duesseldorf.de
>>
>> Tel. +49 (0) 211 81 13074
>>
>> __________________________________________
>>
>>
>> On Mon, Jun 25, 2012 at 4:57 AM, Jarang Hahm <jarang.hahm at gmail.com>wrote:
>>
>>> Dear FieldTrip user.
>>>
>>>
>>>
>>> Hi, I'm processing MEG data of Neuromag 306 system after removing some
>>> bad channels using fieldtrip-20120620 toolbox.
>>>
>>>
>>>
>>> To repair the bad channels with its neighbours, I firstly found the
>>> neighbor of all channel based on distance using 'ft_prepare_neighbours'.
>>>
>>> However, the outcome of neighbour was far more than default distance,
>>> 4cm, from a target channel.
>>>
>>> So, I checked thoroughly the code 'ft_prepare_neighbours', finding it
>>> used information of channel label and position from data’s hdr.grad to find
>>> neighbour of the target.
>>>
>>>
>>>
>>> The problem is channel label and position in hdr.grad are arranged
>>> differently.
>>>
>>> As far as I found, both information come from different source: the
>>> channel label was from code 'fiff_read_meas_info', while the channel
>>> position was from ‘channelposition’ in 'ft_datatype_sens'.
>>>
>>> And  the channel label is sorted into the sensor location, e. g. MEG
>>> 0113, MEG 0112, MEG 0111, MEG 0122, etc, however, the channel position is
>>> arranged along the sensor type (magnetometer and gradiometer) according to
>>> its ending number (1, 2, or 3), e.g. MEG 0111, MEG 0121, MEG 0131, ....,
>>> MEG 0112, MEG 0122, MEG 0132, ...MEG 0113, MEG 0123, MEG 0133, etc.
>>>
>>> Thus, the label and position of channel in hdr.grad were mismatched so
>>> that we got somewhat weired neighbour after using 'ft_prepare_neighbours'.
>>>
>>>
>>> It should be matched correctly to find the proper neighbour and ensure
>>> the result of repair as well.
>>>
>>> In fact, the code 'channelposition' in 'ft_datatype_sens' yield the
>>> channel label as well as the channel position. It might help to solve this
>>> problem.
>>>
>>>
>>>
>>> Is there any other way to solve this problem?
>>>
>>>
>>>
>>>
>>> Best,
>>>
>>>
>>> Jarang Hahm
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> 함자랑 드림.
>
> Jarang Hahm
>
> Interdisciplinary Program in Cognitive Science
> Seoul National University
> Seoul, Korea, Republic of.
> +82-10-9079-3121
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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