freqanalysis_wltconvol.m question

Wed Nov 29 18:20:14 CET 2006

Thanks again,
I have just one last follow-up question:
Why would you square the final ITC?  Tallon-Baudry et al. do not do this in
their j Neurosci. '97 publication.

Brian
At 02:02 AM 11/21/2006, Jan Mathijs Schoffelen wrote:
>Dear Brian et al,
>
>
>----------
>From: Brian Roach [mailto:Brian.Roach at yale.edu]
>Sent: Monday, November 20, 2006 11:56 PM
>To: Jan Mathijs Schoffelen
>Subject: Re: [FIELDTRIP] freqanalysis_wltconvol.m question
>
>Hi, I could not get this posted to the list, and figured since you gave
>most of the feedback, I would see what you think.
>
>thanks,
>Brian
>
>
>Date: Mon, 13 Nov 2006 12:09:00 -0500
>To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>From: Brian Roach <Brian.Roach at yale.edu>
>Subject: Re: [FIELDTRIP] freqanalysis_wltconvol.m question
>Bcc: Daniel Mathalon <daniel.mathalon at yale.edu>
>
>Thanks for the advice,  I am wondering if FT users would agree that this
>is an acceptable way to estimate univariate phase coherence:
>
>In freqanalysis_wltconvol.m, line 283:
>                 %         powdum = (2.* abs(autspctrmacttap)  ./
> data.fsample) .^ 2;
>                 powdum = (2.*autspctrmacttap  ./ data.fsample);
>
>1. I've commented out the power line and inserted basically the same thing
>(but not squared)
>2. As suggested, I change cfg.keeptrials = 'yes';
>3. After running freqanalysis.m, in the command prompt:
>         itc =
> abs(mean(squeeze(freq.powspctrm)./abs(squeeze(freq.powspctrm)),1))
>
>squeeze is used because freq.powspctrm is a 3 d matrix including sites,
>times, and frequencies and in the above case I am just getting itc from 1
>channel.  Does this method seem alright?  Regarding step #1 above, it
>seemed to make no difference whether I left the 2.* in that equation or
>not, which seems consistent with an earlier e-mail that mentioned this
>multiplication being tied into power, so it does not influence phase
>angle.  Is that right?  Or, should it be taken out for my purposes?
>
>thanks,
>Brian
>
>This looks fine to me. Indeed the factor of 2 does not affect the outcome,
>because it falls out in the division (normalization) step.
>
>Yours,
>
>Jan-Mathijs
>
>PS: you might have to think about whether or not to square the final itc,
>to make it consistent with the way it is defined in the literature.
>
>
>
>At 04:37 AM 11/9/2006, you wrote:
>
>Dear Brian,
>
>Freqanalysis_wltconvol does not support fourier as an output. However, since
>wavelet-analysis and fft's in the end are about the same thingy, you could
>use freqanalysis_mtmconvol to achieve your goal.
>There is a tutorial on the fieldtrip-website which deals with this function,
>and uses it in a way that it resembles a wavelet-analysis, in which the
>time-frequency resolution is treated in the same way as with standard
>wavelet-analysis.
>
>Phase-locking-value is defined in fieldtrip as a bivariate-measure, so that
>means that it quantifies how consistent the phase-relation between two
>channels is across trials.
>Inter-trial coherence is a bit an odd thingy, because the term coherence
>suggests something bivariate, but the way you would like to use it, is
>essentially univariate. You want to estimate how consistent the phase of the
>oscillations at a particular channel is across trials.
>However, both measures use similar math. In fact, when you create a
>dummy-fourier-channel you can use the plv-option to obtain your 'itc'. This
>is because in this situation, the mathematics become identical. I would
>advise it like this:
>
>Do your freqanalysis as Robert suggested in one of his previous mails (see
>below (cfg.keeptapers = 'yes')).
>Then create a dummy channel:
>
>dim                             = size(freq.fourierspctrm;
>freq.fourierspctrm(:,end+1,:,:) = ones(dim([1 3 4]));
>freq.label = 'dummy';
>
>cfg = [];
>cfg.cohmethod = 'plv';
>cfg.channelcmb = channelcombination({'dummy' 'all'}, freq.label); %should
>work
>
>itc = freqdescriptives(cfg, freq);
>
>Your 'itc' now is contained in the field itc.cohspctrm;
>
>The check whether this is correctly done is done outside fieldtrip:
>
>itc2 = abs(mean(freq.fourierspctrm./abs(freq.fourierspctrm),1));
>
>Yours,
>
>Jan-Mathijs
>
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Brian Roach
>Sent: Wednesday, November 08, 2006 11:13 PM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] freqanalysis_wltconvol.m question
>
>Robert,
>Thanks for your quick reply.  I did not realize that
>freqanalysis_wltconvol.m allowed for 'fourier' output, but maybe I need to
>download the latest version.  Or, do you mean I should use freqanalysis_mtm
>instead?  Also, how does ITC differ from phase-locking value?  I thought
>they were the same measure.
>At 04:56 PM 11/8/2006, you wrote:
> >Hi Brian
> >
> >On 8 Nov 2006, at 21:20, Brian Roach wrote:
> >>eI would like to take this complex output and use it to calculate
> >>phase-locking factor, but I am not sure what parts of the power
> >>transformation need to be removed - just the abs() and the
> >>squaring?  Clarification of this line of code would be extremely
> >>helpful to me.
> >
> >You can use the existing code for that:
> >
> >For computing the phase-locking value I suggest that you use either
> >   cfg.output='fourier'
> >   cfg.keeptrials='yes'
> >   cfg.keeptapers='yes'
> >or
> >   cfg.output='fourier'
> >   cfg.keeptrials='yes'
> >   cfg.keeptapers='no' (not needed now)
> >   cfg.channelcmb = something, see the help
> >in freqanalysis.
> >
> >Subsequently, use the option
> >   cfg.cohmethod='plv'
> >in freqdescriptives. In case of fourier output in freqanalysis, you
> >should specify the channel combinations here.
> >
> >...
> >Looking back at your previous mail, I see that you mean ITC and not
> >PLV. The stuff above then does not apply. You can do output=fourier
> >in freqanalysis and work manually on the output freq structure. I
> >think that this should work
> >
> >magnitude = abs(freq.fourierspctrm);
> >scaled    = freq.fourierspctrm ./ magnitude;
> >freq.itcspctrm = mean(scaled, 1);
> >freq = rmfield(freq, 'fourierspctrm');   % remove the single
> >fourierspectrum, to avoid confusion
> >freq.dimord = 'chan_freq_time';          % remove the rpt or rpttap
> >dimension
> >
> >best regards,
> >Robert
> >

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