ft_channelrepair with neuromag data

[jan-mathijs schoffelen]

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
>
>
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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
Telephone: 0031-24-3614793


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