[FieldTrip] Single trial baseline correction issues

Jennifer Tellett lpxjrt at nottingham.ac.uk
Tue Jul 21 16:28:45 CEST 2015

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 Tellett
PhD Student
PATCH Study Team

Room C72  |  School of Psychology  |  University Park  |  University of Nottingham  |  NG7 2RD
lpxjrt at nottingham.ac.uk<mailto:lpxjrt at nottingham.ac.uk>  |  0115 84 66610

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