[FieldTrip] Single trial baseline correction issues

[Jennifer Tellett]

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<mailto:lpxjrt at nottingham.ac.uk>  |  0115 84 66610





This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please send it back to me, and immediately delete it. 

Please do not use, copy or disclose the information contained in this
message or in any attachment.  Any views or opinions expressed by the
author of this email do not necessarily reflect the views of the
University of Nottingham.

This message has been checked for viruses but the contents of an
attachment may still contain software viruses which could damage your
computer system, you are advised to perform your own checks. Email
communications with the University of Nottingham may be monitored as
permitted by UK legislation.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150721/d6639372/attachment-0001.html>