[FieldTrip] cluster-based permutation test on WPLI

Zsolt Turi zsoltturi at gmail.com
Wed May 20 22:24:38 CEST 2015


Dear Chris,

thanks again for your comment.

Cheers,
Zsolt

2015-05-19 12:47 GMT+02:00 Cristiano Micheli <michelic72 at gmail.com>:

>
> 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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>>>>
>>>
>>>
>>>
>>> --
>>> ************************************************************
>>> 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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>>>
>>>
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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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>
>
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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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