[FieldTrip] ft_freqstatistics wrong permutation dimension (?)

Tim Guth Guth at mailbox.org
Fri Oct 9 12:02:00 CEST 2020


Dear Jan-Mathijs,

thank you for you reply!

I tried your approach and the code does run through fine with it. By 
pooling over all channels I just try to get a general overview about 
what effects I can find in my data so for this purpose I think it is fine.

Best wishes and thank you very much,

Tim


Am 08.10.2020 um 11:49 schrieb Schoffelen, J.M. (Jan Mathijs):
> Dear Tim,
>
> In order to be able to do (permutation-based) statistics, fieldtrip expects single trial (or single subject) data. I guess that the ‘bookkeeping code’ does not like your creative approach to the permutation scheme.
> I leave it up to you to decide whether it is valid to begin with to use the channel dimension as the dimension across which you’d want to permute, but I would think that you can fool ft_freqstatistics if you cosmetically change the data objects that go into the function:
>
> siz = size(data.powspctrm);
> data.powspctrm = reshape(data.powspctrm,[siz(1) 1 siz(2:3)]); % this squeezes in a singleton ‘chan’ dimension
> data.dimord = ‘rpt_chan_freq_time’;
> data.label = {‘dummy channel’};
>
> If you do this for both conditions’ data structures, I think the code should run through fine. But again, whether this is OK, I don’t know.
>
> Best wishes,
> Jan-Mathijs
>
>
>
>
>> On 7 Oct 2020, at 17:44, Tim Guth <Guth at mailbox.org> wrote:
>>
>> Dear community,
>>
>>
>> my name is Tim Guth and I am working at the University Clinic Freiburg on intracranial EEG data. I am relatively new to fieldtrip and have a question about the function ft_freqstatistics.
>>
>> I tried using it to do a cluster-based permutation test over time-frequency powerspectrum data to compare successfull and non-successfull memory encoding intervals of equal length.
>>
>> I obtained the following two data structures by applying ft_freqanalysis on EEG data from 943 separate channels, averaging the powerspectrum results over trials and then concatenating them in a for loop.
>>
>> allChanSuccEnc =
>>
>>    struct with fields:
>>
>>      powspctrm: [943×50×751 double]
>>          label: {943×1 cell}
>>         dimord: 'chan_freq_time'
>>           time: [1×751 double]
>>           freq: [1×50 double]
>>
>> allChanFailEnc =
>>
>>    struct with fields:
>>
>>      powspctrm: [943×50×751 double]
>>          label: {943×1 cell}
>>         dimord: 'chan_freq_time'
>>           time: [1×751 double]
>>           freq: [1×50 double]
>>
>> I then executed ft_freqstatistics(cfg, allChanSuccEnc, allChanFailEnc) with the following configurations:
>>
>> cfg                            = [];
>> cfg.method             = 'montecarlo';
>> cfg.statistic             = 'indepsamplesT'; % use paired ttest
>> cfg.correctm           = 'cluster';
>> cfg.clusteralpha     = 0.05;
>> cfg.clusterstatistic = 'maxsum';
>> cfg.neighbours       = [];
>> cfg.tail                     = 0;
>> cfg.clustertail        = 0;
>> cfg.alpha                = 0.025;
>> cfg.numrandomization = 500;
>> cfg.latency             = [0, 1.5]; % clusters during encoding period
>> cfg.neighbours      = [];
>> cfg.design               = [ones(1, size(allChanSuccEnc.powspctrm, 1)), ones(1, size(allChanFailEnc.powspctrm, 1)) * 2];
>> cfg.ivar                    = 1;
>>
>> Unfortunately I get the following error message:
>>
>> Error using ft_freqstatistics (line 180)
>> the length of the design matrix (1) does not match the number of observations in the data (2)
>>
>> It seems like the function does not expect input with only one average trial where the permutation has to be done over channels. Do you have any idea how I can perform the permutation test with the channels (and not the trials) being permutet?
>>
>> Thank you for your help
>>
>> Tim
>>
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>> https://doi.org/10.1371/journal.pcbi.1002202
>
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