[FieldTrip] cluster-based permutation test on WPLI
Cristiano Micheli
michelic72 at gmail.com
Tue May 19 12:47:43 CEST 2015
Dear Zsolt,
please find an answer below.
Regards
Cris
On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi <zsoltturi at gmail.com> wrote:
> Hi Tzvetan and Chris,
>
> thanks for your emails.
> Removing channelcmb and adding a new one called label solved my problem.
>
> Chris:
> I'ld like to compare the WPLI difference of two conditions, congruent and
> incongruent ones by using a within-subjects design (so not a between trials
> comparison).
> From your email I may infer that after running wpli, I should still have
> my trials. However, I do not have repetitions (trials) anymore in the
> output structure. Am I doing an illegitimate step during wPLI calculation
> or miss one specification?
>
You did it correctly.
After running the wPLI metric ( I suggest the unbiased version of it, use
the 'wpli_debiased' method in ft_connectivityanalysis) you are left with
no trials. This is because the trials dimension (and tapers) are used to
estimate the phase lag index. If I left that implied in the previous mail,
I did not communicate it very well. What I meant to say is to be careful in
the contrast of two conditions, because the subtraction (or ratio, or
else...) will generate fake effects (or false positives) if the trials in
condition 1 and condition 2 BEFORE wPLI calculation are different.
I hope this helps
Cris
> cfg = [];
> cfg.method = 'wpli';
> dataWPLI = ft_connectivityanalysis(cfg,TFRhann);
>
>
> labelcmb: {9x2 cell}
> dimord: 'chan_freq_time'
> wplispctrm: [9x43x16 double]
> freq: [1x43 double]
> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992
> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1]
> cfg: [1x1 struct]
>
> Thanks for your help!
>
> Best,
> Zsolt
>
>
>
>
> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov <tzvetan.popov at uni-konstanz.de>:
>
>> Hi Zsolt,
>>
>>
>> Hi Tzvetan,
>>
>> thanks for your suggestions.
>> I am still stucked at the ft_freqstatistics, as I keep on receiving the
>> following error and would be glad if you could make a comment on this as
>> well:
>>
>> ####
>> Reference to non-existent field 'label'.
>>
>> Error in ft_freqgrandaverage (line 123)
>> cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label);
>> ###
>>
>> Is it because I have labelcomb in the WPLI data?
>>
>> yes
>>
>>
>> labelcmb: {9x2 cell}
>> dimord: 'chan_freq_time'
>> wplispctrm: [9x7x16 double]
>> freq: [3 4 5 6 7 8 9]
>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992
>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1]
>> cfg: [1x1 struct]
>>
>> And this is my specification (I couldn't fine the option cfg.channelcmb
>> for ft_freqgrandaverage in the reference documentation):
>>
>> again try to give cell arrays as input to ft_freqanalysis. I’m still
>> considering the case you mentioned in your initial e-mail, one channel etc.
>> e.g. cfg.channel = ‘FCzF3’;
>> cfg.parameter = ‘wplispctrm’;
>> cfg.neighbours = []; % this will force clustering over time and
>> freq dimension
>>
>> best
>> tzvetan
>>
>>
>> cfg = [];
>> cfg.keepindividual = 'yes';
>> cfg.cfg.foilim = 'all';
>> cfg.toilim = 'all';
>> cfg.channel = 'all';
>> cfg.parameter = 'wplispctrm';
>>
>> Thanks again for the answer in advance!
>>
>> Best,
>> Zsolt
>>
>> ps.I can provide other parts of my code but I don't want to make this
>> mail too long :
>>
>>
>>
>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov <tzvetan.popov at uni-konstanz.de>:
>>
>>> Hi Zsolt,
>>>
>>>
>>> Dear all,
>>>
>>>
>>> I would like to perform a cluster-based permutation test on weighted
>>> phase lag index values by using a within-subjects experimental design. I
>>> have two conditions (congruent and incongruent one) and my goal is to
>>> compute WPLI between certain channel combinations (FCz and F3 for instance)
>>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the
>>> two conditions.
>>>
>>>
>>> I experienced some difficulties after the point when I calculated the
>>> WPLI data for each participant. To perform the above-mentioned comparison,
>>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test?
>>>
>>> You could. Stick with the tutorial you are currently working with. You
>>> should organize your data into cell arrays and call ft_freqstatistics like
>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}).
>>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise
>>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in
>>> the data.
>>> good luck
>>> tzvetan
>>>
>>>
>>> _______________________________________________
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>>> fieldtrip at donders.ru.nl
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>>>
>>
>>
>>
>> --
>> ************************************************************
>> Ph.D.
>> Department of Clinical Neurophysiology
>> Georg-August University, Göttingen
>> Robert-Koch-Str. 40
>> 37075 Goettingen
>> Web: http://www.uni-goettingen.de/en/222525.html
>> ************************************************************
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>> fieldtrip mailing list
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>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
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>
>
>
> --
> ************************************************************
> Ph.D.
> Department of Clinical Neurophysiology
> Georg-August University, Göttingen
> Robert-Koch-Str. 40
> 37075 Goettingen
> Web: http://www.uni-goettingen.de/en/222525.html
> ************************************************************
>
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> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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