[FieldTrip] Single trial baseline correction issues

[Eelke Spaak]

Hi Jennifer,

Your code should work fine; ft_freqbaseline should support
trial-resolved data. If you look at size(TFRall.powspctrm) both before
and after the baseline correction, does it change? (It should not.) If
it does, could you post the TFRall output of ft_freqanalysis (so
*before* ft_freqbaseline) on e.g. Dropbox and send me a link?

Best,
Eelke

On 22 July 2015 at 08:43, Jennifer Tellett <lpxjrt at nottingham.ac.uk> wrote:
> Hi Agatha,
>
> Thanks for the paper, I had seen that previously and was planning on looking at full epoch single trial baseline correction. However, I am not clear on how such a technique would be implemented using FieldTrip given the difficulties I was having regarding maintaining the single trial information in the structure of the output from ft_freqbaseline. Is this kind of thing possible in FieldTrip or will it require custom coding?
>
> Thanks,
> Jenny
> ________________________________________
> From: Agatha Lenartowicz [alenarto at g.ucla.edu]
> Sent: 21 July 2015 16:07
> To: Tellett Jennifer
> Cc: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] Single trial baseline correction issues
>
> Jennifer. There's an interesting paper out by Arno Delorme on this topic. http://www.ncbi.nlm.nih.gov/pubmed/21994498
>
> Take a look. Agatha On Jul 21, 2015 7:28 AM, Jennifer Tellett <lpxjrt at nottingham.ac.uk> wrote:
>>
>> Hi all,
>>
>> I am relatively new to FieldTrip. I am intending on correlating frontal theta with occipital alpha at single electrode sites on a trial by trial basis for each subject, and as such I was hoping to apply baseline correction at the single trial level as opposed to to the grand average. However, in order to justify the use of the electrode sites, I first created a grand average and did the baseline correction on this. I wanted to check what differences it might make to the grand average if I instead baseline correct each trial, and then compute the grand average instead. However, when I implement ft_freqbaseline, although the dimord still suggests the structure is rpt_chan_freq_time, I no longer have the cumtapcnt variable and if I try to use cfg.avgoverrpts it tells me there are no repeats (trials). This means that (as far as I can see!) I seem to have lost the single trial information in conducting the baseline correction. In addition, because the dimord structure has 'rpt', it won't allow me to use ft_freqgrandaverage on the resulting data.
>>
>> What I'd ideally like is to know what is the best way of implementing baseline correction on a trial-by-trial basis, so that I retain the trial-by-trial information? Can I then create a grand average from these to check whether my justification for electrode choice still stands if baseline correction has been done per trial?
>>
>> Below are the settings I have used for each subject for frequency analysis and baseline correction, let me know if you need any more information.
>>
>>     % establish parameters for frquency analysis
>>     cfg = [];
>>     cfg.output = 'pow';         % chooses what output you want
>>     cfg.channel={'all';'-LIO';'-LHE';'-RHE'};           % chooses which channels to output; all except EOG
>>     cfg.method = 'mtmconvol';   % chooses type of frequency analysis to use
>>     cfg.taper='hanning';        % chooses type of tapering to apply
>>     cfg.foi=2.5:2.5:40;           % chooses frequencies of interest, currently looking between 2.5 and 40 Hz in steps of 2.5
>>     cfg.t_ftimwin= ones(length(cfg.foi),1)*0.5;     % chooses time window of 500ms
>>     cfg.toi= -0.75:0.1:1.65;         % chooses times of interest, currently looking between -0.75 pre stimulus  to 1.65s post-stimulus in steps of 0.1s
>>     cfg.keeptrials='yes';       % chooses whether to give average across trials or to keep individual trial values
>>
>>
>>
>>     %implement the frequency analysis
>>     TFRall = ft_freqanalysis(cfg, data);
>>
>>
>>
>>     %baseline correct
>>     bcfg.baseline = [-0.75 -0.5];
>>     bcfg.baselinetype = 'db';
>>     TFRall = ft_freqbaseline(bcfg, TFRall);
>>
>> I'd really appreciate any ideas on this,
>> Jenny
>>
>> _____________________
>>
>> Jenny Tellett
>> PhD Student
>> PATCH Study Team
>>
>> Room C72  |  School of Psychology  |  University Park  |  University of Nottingham  |  NG7 2RD
>> lpxjrt at nottingham.ac.uk  |  0115 84 66610
>>
>>
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