Fieldtrip question from Piers C

[Jan Mathijs Schoffelen]

Dear Piers,

First of all, I took the liberty to include as a CC to this mail the
FieldTrip discussion list. It might be that some of its members could
positively contribute to answering your questions. You can subscribe to this
list on the fieldtrip-website.

Anyway, currently there is no support for reading in SAM weights files into
fieldtrip. The most important reason for us not having implemented it, is
that we do our source estimation in fieldtrip directly. Perhaps anyone
already has an implementation to directly read in your SAM weights into
matlab (hence the cc to the discussion list). As soon as those weights are
available, it is pretty straightforward to create virtual channel data and
do the subsequent analysis within fieldtrip.
Otherwise a reading routine for SAM weights would be a valuable contribution
to the code.

Another approach would be to use fieldtrip's beamforming algorithm to create
your virtual channels. The 'lcmv'-algorithm is not all too different from
SAM, so you could try this on your specified voxels of interest.

There is a tutorial on the frequency-domain beamformer on the web-site. The
time-domain beamformer needs a slightly different configuration and
input-data.

1 you should use timelockanalysis to compute the covariance of your
bandpass-filtered data.
2 then you can call sourceanalysis, with the output of timelockanalysis as
an input, in combination with a configuration-structure.

Key-elements of this configuration would be:
cfg.method = 'lcmv';
cfg.pos    = Nx3 matrix with x,y,z coordinates of your virtual channels
cfg.reducerank = 2; (necessary for comparability with SAM, and also to give
reasonable results in the first place)
cfg.hdmfile = .hdm file specifying the forward model used

...and I guess some other stuff as well.

Yours,

Jan-Mathijs



-----Original Message-----
From: p.cornelissen at psych.york.ac.uk [mailto:p.cornelissen at psych.york.ac.uk]

Sent: Friday, September 15, 2006 2:54 PM
To: Jan.Schoffelen at fcdonders.ru.nl
Subject: Fieldtrip ? from Piers C


Dear Fieldtrip team,

First - thanks for your excellent software!

I hope its OK for me to ask you a Fieldtrip question.

We have data from an experiment using Aston (UK) universitie's old 151
channel CTF system, and we have used the CTF tools to extract a set of
virtual electrodes, selected on the basis of a robust group SAM analysis.
What we would really like to do is to use our SAM weights files for these
virtual electrodes, to define specific channels in Fieldtrip so that we
can create and compare time*frequency plots from the virtual electrodes in
Fieldtrip.

Any advice on how to do this (preferably by way of example code)would be
deeply appreciated

Regards

Piers Cornelissen