[FieldTrip] clusterstat on multiple frequencies
Zita Eva Patai
eva.patai at psy.ox.ac.uk
Tue Dec 13 18:10:58 CET 2011
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
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