[FieldTrip] connectivity analysis

Bart Michiels michielb at tcd.ie
Fri Dec 20 09:01:13 CET 2013

Good morning Jan-Mathijs,

Some weeks ago you've sent me the following answer to my question on doing
some connectivity and network analysis on some frequency data separated in
frequency bins.
I totally agree with you that electrode level analysis is a bad way for
doing the connectivity analysis, but I have to use electrode level data
(for the moment).

I also listened to your advance and only averaged the connectivity measures
between subjects for the grand average comparison.
For the ft_freqanalysis I used the smoothing box and the foi in such a way
it would overlap my frequency band of interest, but why can't one just
average frequency data for a range of frequencies? And why wouldn't you do
it across trials? For the trials I just used cfg.keeptrials = 'yes' and
used it as an input for ft_connectivityanalysis where the dimension trials
is lost.
So I presume averaging over trials is done in the right way within the
ft_connectivityanalysis function?

Bests, Bart

On 12 November 2013 10:57, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Bart,
> If you 7 frequency bins within each frequency bin are considered to belong
> to the same frequency band, I'd suggest to use the multitaper approach to
> estimate the spectral parameters per frequency band, using just a single
> frequency bin to represent the whole band of interest. So, rather than for
> example estimating from 15 until 21 Hz in steps of 1 Hz, you can also
> estimate only at 18, using cfg.tapsmofrq = 3 in ft_freqanalysis. I suggest
> to have a look at the documentation on the FT-wiki that is concerned with
> frequency analysis. I would certainly not average the spectral
> representation prior to computing the coherence, neither across the
> individual frequency bins, and even more certainly not across trials.
> Regarding statistics, I don't want to discourage you, but I don't think it
> makes sense to attempt doing statistics at the channel level to begin with,
> due to the effects of volume conduction. Also, in any group comparison (but
> also when doing a comparison across conditions), if there is any between
> groups in terms of SNR (e.g. more or less alpha power across groups) you
> are bound to find a statistically significant difference in estimated
> connectivity as well. It remains to be motivated in such a case, that the
> change in estimated connectivity actually reflects a change in true
> connectivity.
> If you want to do statistics irrespective of these caveats, you may want
> to look into FieldTrip's implementation of the non-parametric permutation
> testing framework. There is ample documentation about this on our wiki as
> well.
> Best wishes,
> Jan-Mathijs
> On Oct 30, 2013, at 1:22 PM, Bart Michiels wrote:
> Hi,
> I have 30 patients and 30 controls and I'm investigating their coherence
> (EEG, 128 electrodes). Every patient has ~30 trials resting state eyes open
> consisting of 7 frequency bins with 7 frequencies in each bin. My goal is
> to show connectivity differences between different brain regions in the
> control and patient group (doing electrode-level analysis now, source-level
> analysis is next step).
> - Is it more appropriate to keep the averaging step as the latest step
> (ie. calculate all coherence for all the different subjects, for all
> trials, for all different frequencies in frequency bins) or is it better to
> do the averaging asap (ie. average all frequencies in 1 frequency bin at
> the time-frequency analysis step, average all trials at the
> ft_freqdescriptives step, ...)
> - Is there any better way to do some statistics on the 128x128x7x7 (128
> electrodes, 7 frequency bins, 7 frequencies in each bin) besides using the
> ttest2() matlab function?
> Any tips & tricks are more then welcome!
> Bart
> _______________________________________________
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> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> Jan-Mathijs Schoffelen, MD PhD
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
> http://www.hettaligebrein.nl
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Bart Michiels, Student 2d master,
School of Engineering, Trinity College Institute of Neuroscience and
Trinity Centre for Bioengineering,
Trinity College Dublin,
Dublin 2, Ireland
Email: michielb at tcd.ie <edlalor at tcd.ie>
Web: http://www.mee.tcd.ie/neuraleng/People/Bart<http://www.mee.tcd.ie/neuraleng/People/Ed>
Phone: +353 - 83 443 3315
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