Missing 'elec' field when reading neuroscan CNT files?

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Tue Mar 14 12:22:53 CET 2006

Hi Durk

On 14 Mar 2006, at 11:48, Durk Talsma wrote:
> I just ran into the following issue. For an ongoing EEG project,
> which was originally stored in neuroscan CNT files, I'm trying to
> set up a clusterrandanalysis. The analysis doesn't run, because the
> input data struct is expected  to have an 'elec' field (in order to
> compute the neighbouring channels).
> Just looking at some CTF MEG data, I saw that these data structs do
> contain the (for these puposes) equivalent 'grad' field, consisting
> of the following data members:
> grad.pnt
> grad.ori
> grad.tra
> grad.label
> grad.units
> I suspect that elec will be similar, but which fields are required?
> I suspect pnt, tra, label, and unit. Assuming this is correct, I
> have the following questions:

See the documentation on http://www2.ru.nl/fcdonders/fieldtrip/
_magnetometers_or_gradiometers_described and scroll down to "How are
electrodes, magnetometers or gradiometers described?"

You only need
   elec.pnt   = Nchan x 3, with [x y z]
   elec.label = Nchan x 1 cell array with labels

> In what coordinate system is elec.pnt specified? (Cartesian, polar?
> Which reference frame?)

The positions should be carthesian, and can be in any reference frame
(head/polhemus/mri) and in any units. Whether channels are neighbours
or not will be the same in any reference frame, so that is why that
does not matter. Better not use elec.units, since that is not
consistently supported throughout FieldTrip and probably does not do
anything. In clusterrandanalysis you furthermore can specify
   cfg.neighbourdist = distance in the same units as above

See also read_fcdc_elec (esp look into the code), which might help
you to get an elec structure for your data.

You can also manually construct a neighbourhood structure using
cfg.neighbours (in that case fieldtrip does not need the elec
strucure), that is explained in the help of clusterrandanalysis.

> What is the meaning of the tra field?

It is only for MEG, and it is the linear transformation matrix from
the field at each coil to the field at each channel. Gradiometer
channels have 2 coils, so think of a forward model for all coils that
contains (2*151)x3 fT values, a grad.tra=[eye(151) -eye(151)] and
aforward model for all channels that contains 151x3 fT values (the 3
is because of the three dipole orientations).


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