ft_channelrepair with neuromag data

[Burkhard Maess]

Dear David,

I agree with Jan-Mathijs.

variant a: apply maxfilter - that will repair all broken channels. You
also can manually define certain channels as broken. Maxfilter may also
align data of different headpositions to a single position.

variant b: use megrealign - it includes a minimum norm localization and
from there MEG data is forward computed. In this way, you can repair
channels, align different head positions to the same and even convert
data between different systems.

all the best,
Burkhard


jan-mathijs schoffelen wrote:
> Dear David,
>
> This is a good point. As far as I can see from the code, no
> distinction is made between gradiometers and magnetometers.
> Naively, I would propose the following: first indeed split the data
> into two subset: gradiometers only and magnetometers only, only then
> apply the channel reparation routine. Yet, for the gradiometer subset
> data, it is questionable whether as such the replacement of a bad
> channel with its neighbours makes sense, because this would lead to
> averaging gradients of the magnetic field with an orthogonal orientation.
>
> In other words, this is probably not the most sensible approach. I
> don't think repairing after combining the planar gradients is
>  desired, because this leads to an unwanted amplification of the noise
> (because the combination step results in taking an absolute value).
> Alternatively, you could consider using ft_megrealign, which in
> principle could be used to repair bad channels. The recipe would be to
> only use the data with the clean channels in the input, and you would
> want to interpolate the data back onto the original sensor-array. An
> example for interpolating between two types of CTF-systems is shown
> here http://fieldtrip.fcdonders.nl/example/megrealign.
>
> Just out of curiosity: doesn't the maxfilter in the Neuromag software
> allow for similar things?
>
> Best wishes,
>
> Jan-Mathijs
>
> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>
>> Hi Fieldtrippers,
>>
>> I would like to use ft_channelrepair to interpolate data for some
>> missing/deleted channels with Neuromag 306 data.  I am just wondering
>> whether there are any potential problems with using the nearest
>> neighbor interpolation, given the triplet format of the Neuromag
>> system (two planar gradiometers and one magnetometer).
>>
>> If this is problematic, are there other options to fixing bad/missing
>> channels (e.g., can ft_channelrepair be run on just a subset of the
>> channels, say the gradiometers after I run ft_combineplanar)?
>>
>> Thanks!
>> David
>>
>> --
>> David A. Ziegler
>> Department of Brain and Cognitive Sciences
>> Massachusetts Institute of Technology
>> 43 Vassar St,  46-5121
>> Cambridge, MA  02139
>> Tel: 617-258-0765
>> Fax: 617-253-1504
>> daz at mit.edu <mailto:daz at mit.edu>
>>
>>
>>
>>
>>
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>>
>
> 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 <mailto:J.Schoffelen at donders.ru.nl>
> Telephone: 0031-24-3614793
>
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> You are receiving this message because you are subscribed to
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> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

--
------------------------------------------------------------
Dr. Burkhard Maess
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
Aussenstelle Bennewitz, phone/fax: +49(3425)887525-26/-11
mail: maess 'at' cbs.mpg.de,           http://www.cbs.mpg.de
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You are receiving this message because you are subscribed to
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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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