[FieldTrip] clusterstat on multiple frequencies
Zita Eva Patai
eva.patai at psy.ox.ac.uk
Tue Dec 13 19:18:36 CET 2011
Thank you Matt, that further makes my situation more clear to me!
On Tue, Dec 13, 2011 at 5:47 PM, Matt Mollison <matt.mollison at gmail.com>wrote:
> Hi Zita,
>
> I have not used this method much, but it actually is possible to plot
> clusters without averaging over the frequency dimension
> using ft_multiplotTFR (where cfg.avgoverchan = 'no'; cfg.avgovertime =
> 'no'; cfg.avgoverfreq='no'; in your statistical test—so you'll get space,
> time, and frequency information). You can also highlight the significant
> portions of time and frequency space, using cfg.mask='yes',
> cfg.maskparameter='mask', and set a cfg.maskalpha. Do keep in mind that
> there are important reasons for averaging over frequency, as Dr. Maris
> described in this post (specifically, to increase power): <
> http://mailman.science.ru.nl/pipermail/fieldtrip/2010-November/003312.html
> >.
>
> Cheers,
> Matt
>
> --
> Univ. of Colorado at Boulder
> Dept. of Psychology and Neuroscience
> matthew.mollison at colorado.edu
> http://psych.colorado.edu/~mollison/
>
> On Tue, Dec 13, 2011 at 10:10 AM, Zita Eva Patai <eva.patai at psy.ox.ac.uk>wrote:
>
>> Dear Jan-Mathijs,
>>
>> Thank you for that, it makes a lot more sense. I figured the data was too
>> complex for display, so I will average over frequencies as you suggested,
>> as I am interested in an effect that would encompass that range anyway...
>>
>> Thank you again and happy holidays!
>> z
>>
>> On Tue, Dec 13, 2011 at 4:22 PM, jan-mathijs schoffelen <
>> jan.schoffelen at donders.ru.nl> wrote:
>>
>>> Hi Zita,
>>>
>>> OK. I now understand the point. ft_clusterplot throws an error because
>>> it does not know how to collapse across frequencies. If the clusters have
>>> spectral extent (as well as spatial extent) it's a non-trivial question
>>> what are the channels to be plotted, because different channels can
>>> contribute different time and frequency points to the significant cluster.
>>> The time points are dealt with because ft_clusterplot shows the cluster
>>> evolving over time; the frequencies are not dealt with. FieldTrip does not
>>> make the choice of which channels to highlight for you (should all
>>> frequencies be significant for a given time point, or only one, or just a
>>> few?) and thus throws an error. However, if you have a priori reasons to
>>> expect your effect to occur in a particular frequency range (as you seem to
>>> do, because of your specification of the cfg before calling
>>> ft_freqstatistics), you can also specify cfg.avgoverfreq to 'yes', yielding
>>> a single observation per channel (and by construction the clustering only
>>> occurs over channels), making the plotting trivial.
>>>
>>> I hope this helps.
>>>
>>> BW,
>>>
>>> JM
>>>
>>>
>>>
>>> On Dec 12, 2011, at 12:22 PM, Zita Eva Patai wrote:
>>>
>>> Dear Jan-Mathijs,
>>>
>>> Sorry I was so vague, i thought maybe it was a common problem...
>>>
>>> OK, so i was running a clusterstat with the following input ( main
>>> point, i want to look at the difference between conditions over a set of
>>> frequencies)
>>> ***
>>> load blk1_tf_avg
>>> load blk3_tf_avg
>>>
>>> cfg = [];
>>> cfg.latency = [1.0 1.5 ];
>>> cfg.frequency = [4 8];
>>> cfg.method = 'montecarlo';
>>> cfg.statistic = 'depsamplesT';
>>> cfg.correctm = 'cluster';
>>> cfg.clusteralpha = 0.05;
>>> cfg.clusterstatistic = 'maxsum';
>>> cfg.minnbchan = 2;
>>> cfg.tail = 0;
>>> cfg.clustertail = 0;
>>> cfg.alpha = 0.025;
>>> cfg.numrandomization = 1000;
>>> cfg.feedback = 'yes';
>>> cfg.neighbours = ft_neighbourselection(cfg, blk1_tf_avg);
>>> subj = 15;
>>> design = zeros(2,2*subj);
>>> for i = 1:subj
>>> design(1,i) = i;
>>> end
>>> for i = 1:subj
>>> design(1,subj+i) = i;
>>> end
>>> design(2,1:subj) = 1;
>>> design(2,subj+1:2*subj) = 2;
>>>
>>>
>>> cfg.design = design;
>>> cfg.uvar = 1;
>>> cfg.ivar = 2;
>>>
>>>
>>> [stat] = ft_freqstatistics(cfg, blk3_tf_avg, blk1_tf_avg);
>>>
>>>
>>> save stat_tf_theta_1000_1500_bkey3vsbkey1 stat
>>>
>>>
>>> ***
>>>
>>> The error comes during the plotting phase when it says that i should not
>>> have multiple frequencies, as the data should be averaged across
>>> frequencies. And it does save my file (stat_theta....) but and i can see
>>> the pos/neg clusters in the data structure...but i can't plot with :
>>>
>>> cfg = [];
>>> cfg.highlightsymbolseries = ['*','*','.','.','.'];
>>> cfg.layout = '/Applications/fieldtrip/template/neuromag306mag.lay';
>>> cfg.contournum = 0;
>>> cfg.markersymbol = '.';
>>> cfg.alpha = 0.05;
>>> cfg.zparam = 'stat';
>>> ft_clusterplot(cfg,stat);
>>>
>>>
>>>
>>> I have also tried plotting with the script from the tutorial
>>>
>>>
>>> pos_cluster_pvals = [stat.posclusters(:).prob];
>>> pos_signif_clust = find(pos_cluster_pvals < stat.cfg.alpha);
>>> pos = ismember(stat.posclusterslabelmat, pos_signif_clust);
>>>
>>>
>>> neg_cluster_pvals = [stat.negclusters(:).prob];
>>> neg_signif_clust = find(neg_cluster_pvals < stat.cfg.alpha);
>>> neg = ismember(stat.negclusterslabelmat, neg_signif_clust);
>>>
>>> for k = 1:20;
>>>
>>> etc.
>>> but this makes the plot really weird looking...and i am not sure how i
>>> can only plot the data from the frequencies i would like to display (in
>>> this case 4-8Hz). I know how to make the subtraction image (between my two
>>> conditions), but not how to specify the frequency range that i want
>>> displayed...
>>>
>>> If this is too complicated, is there a way to average over a set of
>>> frequencies in the data, and then just input files into the permutation
>>> test that are already collapsed across the frequency range i am interested
>>> in?
>>>
>>>
>>> Thank you!
>>> z
>>>
>>>
>>> On Mon, Dec 12, 2011 at 7:59 AM, jan-mathijs schoffelen <
>>> jan.schoffelen at donders.ru.nl> wrote:
>>>
>>>> Hi Zita,
>>>>
>>>> Could you provide some more information please? What plotting function
>>>> are you using? What does the stat-structure look like etc.? With sufficient
>>>> additional information we can try and reproduce the problem, and if it's a
>>>> bug fix it. If it's not a bug, we may give you some hints to fool the
>>>> system...
>>>>
>>>> BW,
>>>>
>>>> Jan-Mathijs
>>>>
>>>> On Dec 11, 2011, at 8:28 PM, Zita Eva Patai wrote:
>>>>
>>>> Dear FT-ers,
>>>>
>>>> I have tried to run a permutation test on time-frequency data, and
>>>> would have like to see a statistical evealuation over a set of frequencies
>>>> (ex: 4-8Hz)
>>>>
>>>> It seems that the test itself runs, but it crashes when i try to plot
>>>> the data, saying that 'stat' must not contain multiple frequencies.
>>>>
>>>> I was wondering if there was a way to evaluate the difference between
>>>> two conditions over a set range of frequencies?
>>>>
>>>> Thank you!
>>>> zita
>>>>
>>>>
>>>> --
>>>>
>>>> Zita Patai
>>>> DPhil Candidate, Experimental Psychology
>>>> University of Oxford
>>>> bcl.psy.ox.ac.uk/people/zita-eva-patai/
>>>> eva.patai at psy.ox.ac.uk
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>>
>>>> Jan-Mathijs Schoffelen, MD PhD
>>>>
>>>> Donders Institute for Brain, Cognition and Behaviour,
>>>> Centre for Cognitive Neuroimaging,
>>>> Radboud University Nijmegen, The Netherlands
>>>>
>>>> Max Planck Institute for Psycholinguistics,
>>>> Nijmegen, The Netherlands
>>>>
>>>> J.Schoffelen at donders.ru.nl
>>>> Telephone: +31-24-3614793
>>>>
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>>
>>> --
>>>
>>> Zita Patai
>>> DPhil Candidate, Experimental Psychology
>>> University of Oxford
>>> bcl.psy.ox.ac.uk/people/zita-eva-patai/
>>> eva.patai at psy.ox.ac.uk
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> Jan-Mathijs Schoffelen, MD PhD
>>>
>>> Donders Institute for Brain, Cognition and Behaviour,
>>> Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>>
>>> Max Planck Institute for Psycholinguistics,
>>> Nijmegen, The Netherlands
>>>
>>> J.Schoffelen at donders.ru.nl
>>> Telephone: +31-24-3614793
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> --
>>
>> Zita Patai
>> DPhil Candidate, Experimental Psychology
>> University of Oxford
>> bcl.psy.ox.ac.uk/people/zita-eva-patai/
>> eva.patai at psy.ox.ac.uk
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
Zita Patai
DPhil Candidate, Experimental Psychology
University of Oxford
bcl.psy.ox.ac.uk/people/zita-eva-patai/
eva.patai at psy.ox.ac.uk
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