<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi all,<div><br></div><div>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. </div><div><br></div><div>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?</div><div><br></div><div>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.</div><div><div><br class="webkit-block-placeholder"></div><div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> </span>% establish parameters for frquency analysis</div><div style="margin: 0px; font-size: 10px; font-family: Courier; "> cfg = [];</div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.output = </span><span style="color: #b245f3">'pow'</span><span style="color: #000000">; </span>% chooses what output you want</div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.channel={</span><span style="color: #b245f3">'all'</span><span style="color: #000000">;</span><span style="color: #b245f3">'-LIO'</span><span style="color: #000000">;</span><span style="color: #b245f3">'-LHE'</span><span style="color: #000000">;</span><span style="color: #b245f3">'-RHE'</span><span style="color: #000000">}; </span>% chooses which channels to output; all except EOG</div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.method = </span><span style="color: #b245f3">'mtmconvol'</span><span style="color: #000000">; </span>% chooses type of frequency analysis to use</div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.taper=</span><span style="color: #b245f3">'hanning'</span><span style="color: #000000">; </span>% chooses type of tapering to apply</div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.foi=2.5:2.5:40; </span>% chooses frequencies of interest, currently looking between 2.5 and 40 Hz in steps of 2.5</div><div style="margin: 0px; font-size: 10px; font-family: Courier; "> cfg.t_ftimwin= ones(length(cfg.foi),1)*0.5; <span style="color: #25992d">% chooses time window of 500ms</span></div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.toi= -0.75:0.1:1.65; </span>% chooses times of interest, currently looking between -0.75 pre stimulus to 1.65s post-stimulus in steps of 0.1s</div><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> cfg.keeptrials=</span><span style="color: #b245f3">'yes'</span><span style="color: #000000">; </span>% chooses whether to give average across trials or to keep individual trial values</div><p style="margin: 0px; font-size: 10px; font-family: Courier; min-height: 12px; "> <br class="webkit-block-placeholder"></p><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> </span>%implement the frequency analysis</div><div style="margin: 0px; font-size: 10px; font-family: Courier; "> TFRall = ft_freqanalysis(cfg, data);</div><p style="margin: 0px; font-size: 10px; font-family: Courier; min-height: 12px; "> <br class="webkit-block-placeholder"></p><div style="margin: 0px; font-size: 10px; font-family: Courier; color: rgb(37, 153, 45); "><span style="color: #000000"> </span>%baseline correct</div><div style="margin: 0px; font-size: 10px; font-family: Courier; "> bcfg.baseline = [-0.75 -0.5];</div><div style="margin: 0px; font-size: 10px; font-family: Courier; "> bcfg.baselinetype = <span style="color: #b245f3">'db'</span>;</div><div style="margin: 0px; font-size: 10px; font-family: Courier; "> TFRall = ft_freqbaseline(bcfg, TFRall);</div></div><div><br></div><div>I'd really appreciate any ideas on this,</div><div>Jenny</div><div><br></div><div apple-content-edited="true">
_____________________<br><br>Jenny Tellett<br>PhD Student<br>PATCH Study Team<br><br>Room C72 | School of Psychology | University Park | University of Nottingham | NG7 2RD<br><a href="mailto:lpxjrt@nottingham.ac.uk">lpxjrt@nottingham.ac.uk</a> | 0115 84 66610
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