[FieldTrip] calculating behavioural-power correlation
Hwee Ling Lee
hweeling.lee at gmail.com
Tue Feb 17 17:39:29 CET 2015
Thanks! One last question, just to be sure, what is the reference for this
correlation method? I tried to search for your publications but not sure
which one to cite.
Cheers,
Hweeling
On 17 February 2015 at 16:44, arjen stolk <a.stolk8 at gmail.com> wrote:
> Yes it does. ;)
> Arjen
>
>
>
> -------- Oorspronkelijk bericht --------
> Van: Hwee Ling Lee <hweeling.lee at gmail.com>
> Datum:
> Aan: "Stolk, A. (Arjen)" <a.stolk at donders.ru.nl>
> Cc: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Onderwerp: Re: [FieldTrip] calculating behavioural-power correlation
>
>
> Dear Arjen,
>
> Thanks! It works well now.
>
> I plotted the results using ft_clusterplot, and it only shows the
> significant clusters that show significant correlation of power and
> behavioural measure, right? Or is there a better way I can display the
> results?
>
> Thanks again.
>
> Cheers,
> Hweeling
>
>
>
> On 17 February 2015 at 11:45, Stolk, A. (Arjen) <a.stolk at donders.ru.nl>
> wrote:
>
>> Hey Hweeling,
>>
>> "Just to ensure that I get this right, I should create a variable for the
>> behavioural measure such that the variable contains a powspctrm field with
>> the behavioural information for every frequency?"
>> > indeed
>>
>> "What I'm confused is that in the walkthrough website, under the
>> subsection on correlation, it is suggested to create the cfg.design with
>> the behavioural measure that one wants to correlate. So is this information
>> in the walkthrough website incorrect?"
>> > the walkthough may refer to a GLM-based statistical implementation, for
>> which the FT implementation differs from the correlationT statfun. Namely,
>> the former uses the behavioral measure as a regressor in a data model
>> whereas the latter uses the behavioral measure as a datapoint series for
>> correlation with another datapoint series (and then converts to a T value).
>> The correlationT statfun is relatively 'new', hence not yet addressed in
>> the walkthrough.
>>
>> Yours,
>> arjen
>>
>> ------------------------------
>> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
>> on behalf of Hwee Ling Lee [hweeling.lee at gmail.com]
>> *Sent:* Tuesday, February 17, 2015 11:34 AM
>> *To:* FieldTrip discussion list
>>
>> *Subject:* Re: [FieldTrip] calculating behavioural-power correlation
>>
>> Dear Arjen,
>>
>> Thanks for the prompt reply again!
>>
>> Just to ensure that I get this right, I should create a variable for
>> the behavioural measure such that the variable contains a powspctrm field
>> with the behavioural information for every frequency?
>>
>> What I'm confused is that in the walkthrough website, under the
>> subsection on correlation, it is suggested to create the cfg.design with
>> the behavioural measure that one wants to correlate. So is this information
>> in the walkthrough website incorrect?
>>
>> Cheers,
>> Hweeling
>>
>>
>> On 17 February 2015 at 11:23, Stolk, A. (Arjen) <a.stolk at donders.ru.nl>
>> wrote:
>>
>>> Hey Hweeling,
>>>
>>> It seems you're only inserting one input variable into the statistics
>>> function, i.e. "[c200_delta_stat] = ft_freqstatistics(cfg,
>>> sub_LF_c200{:});"
>>>
>>> Could you try something along this line: ft_freqstatistics(cfg, freq1,
>>> freq2)
>>>
>>> where freq1 is the original freq data, and freq2 is a copy of freq but
>>> with the relevant values (say, in powspctrm) replaced with behavior values
>>> (ensure this behavior matrix is matched in terms of size and dimensions to
>>> the original freq values).
>>>
>>> Hope this helps,
>>> Arjen
>>>
>>> --
>>> Donders Institute for Brain, Cognition and Behaviour
>>> Centre for Cognitive Neuroimaging
>>> Radboud University Nijmegen
>>>
>>> Email: a.stolk at donders.ru.nl
>>> <https://mail.ru.nl/owa/redir.aspx?C=aE7VYn0S90OKCrgPeLfE1S7ZybNAtNEIa36fR052GideznKNfSHe2KSW6d9DoW6tEIOMlaBdT-s.&URL=mailto%3aa.stolk%40donders.ru.nl>
>>> Phone: +31(0)243 68294
>>> Web: www.arjenstolk.nl
>>> <https://mail.ru.nl/owa/redir.aspx?C=aE7VYn0S90OKCrgPeLfE1S7ZybNAtNEIa36fR052GideznKNfSHe2KSW6d9DoW6tEIOMlaBdT-s.&URL=http%3a%2f%2fwww.arjenstolk.nl>
>>> ------------------------------
>>> *From:* Hwee Ling Lee [hweeling.lee at gmail.com]
>>> *Sent:* Tuesday, February 17, 2015 10:33 AM
>>> *To:* Stolk, A. (Arjen)
>>> *Cc:* FieldTrip discussion list
>>> *Subject:* Re: [FieldTrip] calculating behavioural-power correlation
>>>
>>> Dear Arjen,
>>>
>>> Thanks for the prompt reply. I keep getting an error message when I
>>> set up my correlation cluster statistics, and I'm not sure what I could
>>> have done wrong. Here's my script:
>>>
>>> cfg = [];
>>> cfg.layout = 'EEG1010.lay';
>>> cfg.neighbours = neighbours;
>>> cfg.channel = 'all';
>>> cfg.latency = 'all';
>>> cfg.avgovertime = 'no';
>>> cfg.avgoverchan = 'no';
>>> cfg.avgoverfreq = 'yes';
>>> cfg.parameter = 'powspctrm';
>>> cfg.method = 'montecarlo';
>>> cfg.statistic = 'ft_statfun_correlationT';
>>> cfg.correctm = 'cluster';
>>> cfg.clusteralpha = 0.05;
>>> cfg.clusterstatistics = 'maxsum';
>>> cfg.minnbchan = 2;
>>> cfg.tail = 0;
>>> cfg.clustertail = 0;
>>> cfg.alpha = 0.025;
>>> cfg.numrandomization = 1000;
>>> cfg.ivar = 1;
>>> cfg.uvar = 1;
>>>
>>> % design matrices
>>> clear design;
>>> % change in MMSE score relative to baseline
>>> design(1,:) = [0.095238095 -0.045454545 -0.533333333 0.238095238
>>> -0.157894737 0.117647059];
>>> design(2,:) = 1:6;
>>> cfg.design = design;
>>>
>>> % for delta band
>>> cfg.frequency = [2 4];
>>> [c200_delta_stat] = ft_freqstatistics(cfg, sub_LF_c200{:});
>>> [c210_delta_stat] = ft_freqstatistics(cfg, sub_HF_c210{:});
>>>
>>> Here's the output from Matlab:
>>>
>>> computing statistic over the frequency range [2.000 4.000]
>>> the call to "ft_appendfreq" took 0 seconds
>>> the call to "ft_selectdata" took 0 seconds
>>> using "ft_statistics_montecarlo" for the statistical testing
>>> using "ft_statfun_correlationT" for the single-sample statistics
>>> constructing randomized design
>>> total number of measurements = 6
>>> total number of variables = 2
>>> number of independent variables = 1
>>> number of unit variables = 1
>>> number of within-cell variables = 0
>>> number of control variables = 0
>>> using a permutation resampling approach
>>> repeated measurement in variable 1 over 6 levels
>>> number of repeated measurements in each level is 1 1 1 1 1 1
>>> computing a parametric threshold for clustering
>>> Error using ft_statfun_correlationT (line 90)
>>> Invalid specification of the design array.
>>> Error using ft_statistics_montecarlo (line 254)
>>> could not determine the parametric critical value
>>> for clustering
>>>
>>> Error in ft_freqstatistics (line 319)
>>> [stat, cfg] = statmethod(cfg, dat, cfg.design);
>>>
>>> Would you please tell what I have done wrong in this case?
>>>
>>> Thanks!
>>>
>>> Cheers,
>>> Hweeling
>>>
>>>
>>> On 17 February 2015 at 10:18, Stolk, A. (Arjen) <a.stolk at donders.ru.nl>
>>> wrote:
>>>
>>>> Hi Hweeling,
>>>>
>>>> Have a look at the help of ft_statfun_correlationT, which might be the
>>>> function you're looking for. This function calculates correlations between
>>>> two variables (e.g. subjects' behaviors and brain activities) and converts
>>>> the resulting correlation coefficients to t-statistics.
>>>>
>>>> Best,
>>>> arjen
>>>>
>>>> --
>>>> Donders Institute for Brain, Cognition and Behaviour
>>>> Centre for Cognitive Neuroimaging
>>>> Radboud University Nijmegen
>>>>
>>>> Email: a.stolk at donders.ru.nl
>>>> <https://mail.ru.nl/owa/redir.aspx?C=aE7VYn0S90OKCrgPeLfE1S7ZybNAtNEIa36fR052GideznKNfSHe2KSW6d9DoW6tEIOMlaBdT-s.&URL=mailto%3aa.stolk%40donders.ru.nl>
>>>> Phone: +31(0)243 68294
>>>> Web: www.arjenstolk.nl
>>>> <https://mail.ru.nl/owa/redir.aspx?C=aE7VYn0S90OKCrgPeLfE1S7ZybNAtNEIa36fR052GideznKNfSHe2KSW6d9DoW6tEIOMlaBdT-s.&URL=http%3a%2f%2fwww.arjenstolk.nl>
>>>> ------------------------------
>>>> *From:* fieldtrip-bounces at science.ru.nl [
>>>> fieldtrip-bounces at science.ru.nl] on behalf of Hwee Ling Lee [
>>>> hweeling.lee at gmail.com]
>>>> *Sent:* Tuesday, February 17, 2015 10:06 AM
>>>> *To:* FieldTrip discussion list
>>>> *Subject:* [FieldTrip] calculating behavioural-power correlation
>>>>
>>>>
>>>> Dear all,
>>>>
>>>> I read on the "walkthrough" that it is possible to calculate
>>>> behavioural-power correlation across subjects. However, I was not sure what
>>>> type of descriptive statistics (i.e. cfg.statistics) I should use when
>>>> performing correlation cluster statistics.
>>>>
>>>> Would someone please enlighten me which type of statistics I should
>>>> input for cfg.statistics?
>>>>
>>>> Thanks!
>>>>
>>>> Best regards,
>>>> Hweeling
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>
>
> --
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de
> Email 2: hweeling.lee<at>gmail.com
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================
>
--
=================================================
Dr. rer. nat. Lee, Hwee Ling
Postdoc
German Center for Neurodegenerative Diseases (DZNE) Bonn
Email 1: hwee-ling.lee<at>dzne.de
Email 2: hweeling.lee<at>gmail.com
https://sites.google.com/site/hweelinglee/home
Correspondence Address:
Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
=================================================
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