[FieldTrip] Antw: Re: WPLI weighted phase-locking index: available in fieldtrip? (Gregor Volberg)
Gregor Volberg
Gregor.Volberg at psychologie.uni-regensburg.de
Thu Feb 17 10:57:37 CET 2011
Dear Martin,
thanks a lot for your help! I will try it within the next days.
Best regards,
Gregor
--
Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de> ( mailto:gregor.volberg at psychologie.uni-regensburg.de )
University of Regensburg
Institute for Experimental Psychology
93040 Regensburg, Germany
Tel: +49 941 943 3862
Fax: +49 941 943 3233
http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
>>> Martin Vinck <martinvinck at gmail.com> 2/17/2011 9:43 AM >>>
Dear Gregor,
Thank you for your interest.
Please find, in the latest release, the WPLI functionality in
ft_connectivityanalysis.
Best regards,
Martin Vinck.
On Feb 11, 2011, at 10:46 AM, fieldtrip-request at donders.ru.nl wrote:
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> Today's Topics:
>
> 1. Re: Fwd: Modification of ft_timelockgrandaverage
> cfg.keepindividual (Lucie Charles)
> 2. WPLI weighted phase-locking index: available infieldtrip?
> (Gregor Volberg)
> 3. bug in ft_componentanalysis (Baptiste Gauthier)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 Feb 2011 14:03:30 +0100
> From: Lucie Charles <lucie.charles.ens at googlemail.com>
> To: Email discussion list for the FieldTrip project
> <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Fwd: Modification of ft_timelockgrandaverage
> cfg.keepindividual
> Message-ID:
> <AANLkTi=m90GkTFMb_=44HMGLuriGGz-mw4eBBawWTZGJ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you very much for this very detailed response.
>
> I didn't know (or forgot) that ft_timelockstatistics could take
> several data
> sets as an input (I thought we always needed the big data matrix
> with all
> the subjects). That makes much more sense to remove the option in this
> context.
>
> Thanks again,
>
> Lucie
>
> 2011/2/10 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
>
>> Dear Lucie,
>>
>> Thank you very much for your feedback. I take the liberty to anyhow
>> post
>> this to the discussion list, so that other people may take notice /
>> join in
>> the discussion / etc.
>>
>> Thanks a lot for this quick response : I understand the logic
>> behind this.
>> It's true that I noticed some inconsistencies due to the
>> interpretation of
>> the field dimord which can't be well defined if you have both
>> individual and
>> average data in your structure.
>>
>>
>> OK
>>
>> However, I think many people were happy with this option as it was.
>> It's
>> quite handy to keep both the average and individual data because
>> you can
>> compute statistics and at the same time you don't have to redo the
>> average
>> every time. I think a lot of scripts rely on that at least in our
>> lab.
>>
>>
>> The historical purpose for supporting cfg.keepindividual = 'yes',
>> was in
>> order to get a representation of all single subjects' data in a
>> single data
>> matrix: data.individual. Nowadays, ft_timelockstatistics supports
>> multiple
>> data structures in the input, i.e. ft_timelockstatistics(cfg,
>> subj1, subj2
>> subj3, etc) so I think the call to ft_timelockgrandaverage could
>> even be
>> bypassed.
>> The FieldTrip development team is very keen on providing backward
>> compatibility support. While in general this is feasible for the
>> functions
>> which are in FieldTrip, it is very difficult to realize for lab-
>> specific
>> scripts. In this particular example I think that clarity of the data
>> representation should prevail over backward compatibility issues,
>> particularly because in this case there's an easy workaround: just
>> call
>> ft_timelockgrandaverage twice. Moreover, a clean and unambiguous data
>> representation is a prerequisite for further developing the
>> software, and
>> keeping the historical 'oddity' will only hamper code development.
>>
>> Furthermore, it's a bit strange to have a function called
>> ft_timelockgrandaverage which doesn't compute any grandaverage in
>> some cases
>> !
>>
>>
>> I agree, yet see my point above. Some people may just like to have
>> the data
>> represented in a single matrix.
>>
>>
>> I would suggest to keep the function as it is but add more options
>> (such as
>> cfg.dimord = 'avg' or 'individual') to make the experimenter aware
>> of this
>> issue and to solve further computation problem.
>>
>>
>> I hope I could convince you that our philosophy makes sense and
>> that you
>> and your lab-mates are willing to make the effort of adjusting the
>> scripts a
>> bit for future analyses. If very problematic, I would advice for
>> the current
>> analyses to rely on an old version of ft_timelockgrandaverage.
>>
>> Best wishes,
>>
>> Jan-Mathijs
>>
>>
>>
>> Thank you again,
>>
>> Lucie
>>
>> PS : I've sent this email only to you as this is just a suggestion
>> which
>> might not be relevant for all users.
>>
>>
>> 2011/2/10 jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
>>
>>> Dear Lucie,
>>>
>>> Yes, indeed this has recently been changed. The logic behind it is
>>> the
>>> following:
>>>
>>> One either typically wants to keep the individuals, OR the average.
>>>
>>> If in your case you need the average, you have to specify
>>> cfg.keepindividual = 'no';
>>>
>>> Keeping both the average and the individual leads to an inconsistent
>>> definition of the data structure.
>>> The field 'dimord' does not allow for an unequivocal
>>> interpretation of
>>> both indidual and avg are present.
>>>
>>> If you need both the individual, and the avg, you now need to run
>>> ft_timelockgrandaverage twice, once with cfg.keepinididual =
>>> 'yes', and once
>>> with cfg.keepindividual = 'no';
>>>
>>> Best wishes,
>>>
>>> Jan-Mathijs
>>>
>>>
>>> On Feb 10, 2011, at 11:58 AM, Lucie Charles wrote:
>>>
>>> Hello everyone,
>>>
>>> It seems that there has been a modification of
>>> ft_timelockgrandaverage :
>>> now if you specify cfg.keepindividual = 'yes', the grandaverage is
>>> computed
>>> but is not included in the output of the function (see above).
>>>
>>> Why is that ? Many of my scripts rely on this option and I wanted
>>> to know
>>> if there was a good reason for it.
>>>
>>> Thanks,
>>>
>>> Lucie
>>>
>>> New version of ft_timelockgrandaverage (downloaded yesterday), line
>>> 159-176
>>>
>>> %--------------------------------------------
>>> % % collect the results
>>> %--------------------------------------------
>>>
>>> grandavg = [];
>>> grandavg.label = cfg.channel; % cell-array
>>> %grandavg.fsample = varargin{1}.fsample; % fsample is obsolete
>>> grandavg.time = ResultsTime; % 1 x Nsamples
>>>
>>> %KEEP INDIVIDUAL MEANS?
>>> if strcmp(cfg.keepindividual, 'yes')
>>> * grandavg.individual = avgmat; % Nsubj x Nchan x Nsamples
>>> grandavg.dimord = 'subj_chan_time';*
>>> else
>>> * grandavg.avg = ResultGrandavg; % Nchan x Nsamples*
>>> grandavg.var = ResultVar; % Nchan x Nsamples
>>> grandavg.dimord = 'chan_time';
>>> end
>>>
>>> Older version of ft_timelockgrandaverage (april 2010)
>>>
>>> %--------------------------------------------
>>> % % collect the results
>>> %--------------------------------------------
>>>
>>> %SWITCH CHANNEL TO LABEL?
>>> grandavg.label = cfg.channel; % cell-array
>>> grandavg.fsample = varargin{1}.fsample;
>>> grandavg.avg = ResultGrandavg; % Nchan x Nsamples
>>> grandavg.var = ResultVar; % Nchan x Nsamples
>>> grandavg.time = ResultsTime; % 1 x Nsamples
>>>
>>> %KEEP INDIVIDUAL MEANS?
>>> if strcmp(cfg.keepindividual, 'yes')
>>> grandavg.individual = avgmat; % Nsubj x Nchan x Nsamples
>>> grandavg.dimord = 'subj_chan_time';
>>> else
>>> grandavg.dimord = 'chan_time';
>>> end
>>>
>>>
>>> --
>>> Lucie CHARLES
>>>
>>> INSERM-CEA Cognitive Neuroimaging unit
>>>
>>> CEA/SAC/DSV/DRM/NeuroSpin
>>> B?t 145, Point Courrier 156
>>> F-91191 Gif/Yvette, FRANCE
>>> Tel : +33 1 69 08 99 74
>>> Fax : +33 1 69 08 79 73
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> Dr. J.M. (Jan-Mathijs) Schoffelen
>>> Donders Institute for Brain, Cognition and Behaviour,
>>> Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>> J.Schoffelen at donders.ru.nl
>>> Telephone: 0031-24-3614793
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> --
>> Lucie CHARLES
>>
>> INSERM-CEA Cognitive Neuroimaging unit
>>
>> CEA/SAC/DSV/DRM/NeuroSpin
>> B?t 145, Point Courrier 156
>> F-91191 Gif/Yvette, FRANCE
>> Tel : +33 1 69 08 99 74
>> Fax : +33 1 69 08 79 73
>>
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> Lucie CHARLES
>
> INSERM-CEA Cognitive Neuroimaging unit
>
> CEA/SAC/DSV/DRM/NeuroSpin
> B?t 145, Point Courrier 156
> F-91191 Gif/Yvette, FRANCE
> Tel : +33 1 69 08 99 74
> Fax : +33 1 69 08 79 73
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> ------------------------------
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> Message: 2
> Date: Fri, 11 Feb 2011 09:46:51 +0100
> From: "Gregor Volberg" <Gregor.Volberg at psychologie.uni-regensburg.de>
> To: "FieldTrip List" <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] WPLI weighted phase-locking index: available in
> fieldtrip?
> Message-ID: <4D55058B020000570000882D at gwsmtp1.uni-regensburg.de>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Dear fieldtrip developers,
>
> I was just reading the pre-print of an upcoming article in
> Neuroimage by Martin Vinck, Robert Oostenveld et al., "An improved
> index of phase-synchronization...". As I understand, the proposed
> phase-locking index WPLI is not complicated by volume conduction,
> and an unbiased version of the WPLI can be computed that is not
> affected by trial number. This would be exactely what I need for the
> analysis of data from a spatial cueing paradigm.
>
> In the last paragraph, it is announced that the WPLI is made
> available in the fieldtrip toolbox. However, I did not yet find it
> (i was searching for it as an option in ft_connectivityanalysis,
> last Friday's fieldtrip version). May I ask whether it is planned to
> include WPLI / debiased WPLI into that function? Or was it perhaps
> intended to be computed by hand from the cross-spectrum.
>
> Thanks a lot,
> Gregor
> --
> Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de
> > ( mailto:gregor.volberg at psychologie.uni-regensburg.de )
> University of Regensburg
> Institute for Experimental Psychology
> 93040 Regensburg, Germany
> Tel: +49 941 943 3862
> Fax: +49 941 943 3233
> http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
>
>
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> ------------------------------
>
> Message: 3
> Date: Fri, 11 Feb 2011 10:46:13 +0100
> From: Baptiste Gauthier <gauthierb.ens at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] bug in ft_componentanalysis
> Message-ID:
> <AANLkTinBvzzMTF3g7zd=3Jaihg1mSjq1cAOZ2NAGCAh0 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Fieldtrip users,
>
> I noticed a little error in ft_componentanalysis since your latest
> update
> (2011/02/09) :
> While using the function, I got this error message :
>
> "??? Error using ==> toc
> You must call TIC without an output argument before calling TOC
> without an
> input argument.
>
> Error in ==> ft_componentanalysis at 465
> fprintf('total time in componentanalysis %.1f seconds\n', stopwatch
> (toc));
>
> Error in ==> temprod_NEW_runicaonspectra at 37
> comp = ft_componentanalysis(cfg,data);"
>
> It seems there's here a bad use of function toc.m
>
> It should be : "fprintf('total time in componentanalysis %.1f seconds
> \n',
> toc(stopwatch));"
> I tried it and it worked fine.
>
> Please let me know if I'm wrong.
>
> Cheers,
>
> Baptiste gauthier
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