coherence normalization

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Fri Oct 22 17:55:17 CEST 2004

Hi Tom

On 22 Oct 2004, at 17:15, Tom Holroyd wrote:

> Yes.  What I finally did was to export the coherence volumes to
> AFNI, and run an ANOVA (four conditions by eight subjects; it
> took 24 hours for Matlab to calculate the volumes at 1 cm
> resolution, and I don't even have as many trials as I would
> like).  The means across conditions of course show the refdip
> source but the contrasts in the ANOVA (which are basically
> subtractions) nicely cancelled them out, leaving cool-looking
> effects.  :-)

Sounds interesting. But why are you running an ANOVA? The coherence in
a voxel will not be normally distributed. Furthermore, it does not
allow for a decent multiple comparison correction (except bonferoni),
since GRFT does not apply. Did you try sourcestatistics with method
randomization or randcluster? They do multiple comparison correction.

> Now, how can I extract the phase?  Is that stored somehere?

Hmm, no it's not, neither is the orientation. Source.avg.coh is only
the coherence in the dominant direction. I think that the
sourceanalysis option keepcsd=yes will help you here, but am not 100%
sure (should look into it). Conceptually, there are 6 dipoles (2*xyz)
and hence a 6x6 cross-spectral density matrix will be returned as
source.avg.csd (cell-array). That will tell you exactly what the
coherence is in which combination of directions of the two source

Sofar no one ever asker me for the phase, but it would be interesting
to do some more postprocessing of the source.avg.csd matrices to make
something like phase easier to plot. I would like to hear suggestions.
(Same applies for beamed power, where there is also a dominant dipole
orientation which is neglecetd sofar).

best regards

PS there are some "hidden" options for paralellization in Fieldtrip, of
which not all code is shared under GPL. Contact me directly if you have
a bunch of linux nodes and if you are interested.

Robert Oostenveld, PhD
Center for Sensory-Motor Interaction (SMI)
Aalborg University, Denmark


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