TopoplotER for Neuromag 306

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Mon Mar 16 22:07:23 CET 2009

Hi Laurence,

On 11 Mar 2009, at 15:58, Laurence Hunt wrote:
> Quick question from a Fieldtrip newbie - when using topoplotER on
> neuromag 306 data, it appears to give unreasonable results. I
> suspect this is most likely because two out of three sensors are
> magnetometers, whereas every third sensor is a planar gradiometer,
> and the scales on these two types of sensor are different by a
> factor of ten.

That is most likely correct. If you are plotting physical data (i.e.
not some sort of normalized statistic), the planar gradiometers have T/
m units and the magnetometers have T units.

> One thing I could do is edit prepare_layout to only return planar
> gradiometers or magnetometers, but before I do this, do people have
> any other solutions for combining these two different types of
> sensor that they already use for neuromag data?

you can use chantype to select the planar and magnetometers. It would
indeed be nice to have a cfg.chantype option in plrepare layout, where
if specified different from 'all' would use a subset of channels.

Another function that you shoudl look into is combineplanar. We use
that for the ctf data, where in megplanar we convert the axial
gradients in planar gradients. Then we do spectral estimation, and
after that we do combineplanar to combine the power of the 2 planar
(horizontal and vertical) channel at each location. I am not sure
whether it will work out of the box for neuromag data (it was
initially written for ctf data), but rudimentary support for neuromag
is present. That should not be difficult to improve if needed, see
line 205 where the two planar channel sets are determined. The
planarchannelset helper function contaimns hard-coded lists, from
which I am not sure whether they apply precisely the same to all
neuromag systems (this list was determined from a particular system).

best regards,

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