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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Victoria,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I don’t know if this will address your problem; but I think it might depend on the order of your pipeline because if you use PCA at any point before interpolating,
you will be reducing the dimensionality of your data; and interpolation (and presumably combining gradiometers) relies on the data from neighbouring channels to be linearly related.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In my pipeline, I’ve visually rejected trials and channels, then run ICA, then interpolated; I don’t know if that would address your issues?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hope you get it sorted<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Kelly<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>victoria schroeder<br>
<b>Sent:</b> 07 March 2016 20:47<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> [FieldTrip] ft_combineplanar after ft_channelrepair<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hey Fieldtrip users,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am working with neuromag data 306 channels. I would like to interpolate channels using ft_channelrepair. Afterwards it would be good to combine the gradiometers to create planar gradients. However, unfortunately i get an error message
when trying to use ft_combineplanar when i have used ft_channelrepair. Without using ft_channelrepair things work well. Can these two functions not be used on the same data? (See the code and the error message below)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thank you a lot<o:p></o:p></p>
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<p class="MsoNormal">Victoria<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">%prepare neighbours<o:p></o:p></p>
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<p class="MsoNormal">cfg_neighb = [];<o:p></o:p></p>
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<p class="MsoNormal">cfg_neighb.feedback = 'yes';<o:p></o:p></p>
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<p class="MsoNormal">cfg_neighb.method = 'triangulation';<o:p></o:p></p>
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<p class="MsoNormal">cfg_neighb.layout = 'neuromag306all.lay';<o:p></o:p></p>
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<p class="MsoNormal">neighbours = ft_prepare_neighbours(cfg_neighb, dat_orig);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">% Interpolate and put into new data structure<o:p></o:p></p>
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<p class="MsoNormal">cfg = [];<o:p></o:p></p>
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<p class="MsoNormal">cfg.badchannel = { 'MEG1122', 'MEG1312','MEG1411'};<o:p></o:p></p>
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<p class="MsoNormal">cfg.layout = 'neuromag306all.lay';<o:p></o:p></p>
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<p class="MsoNormal">cfg.method = 'nearest';<o:p></o:p></p>
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<p class="MsoNormal">cfg.neighbours = neighbours;<o:p></o:p></p>
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<p class="MsoNormal">Chan_clean = ft_channelrepair(cfg,data_orig);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">data=Chan_clean;<o:p></o:p></p>
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<p class="MsoNormal">%time frequency analysis<o:p></o:p></p>
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<p class="MsoNormal">cfg = [];<o:p></o:p></p>
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<p class="MsoNormal">cfg.output = 'pow';<o:p></o:p></p>
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<p class="MsoNormal">cfg.channel = 'MEGGRAD';<o:p></o:p></p>
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<p class="MsoNormal">cfg.method = 'mtmconvol';<o:p></o:p></p>
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<p class="MsoNormal">cfg.taper = 'hanning';<o:p></o:p></p>
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<p class="MsoNormal">cfg.foi = [2:2:30];<o:p></o:p></p>
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<p class="MsoNormal">cfg.toi = [-1.3:0.05:1]; <o:p></o:p></p>
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<p class="MsoNormal">cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; <o:p></o:p></p>
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<p class="MsoNormal">cfg.keeptrials = 'yes';<o:p></o:p></p>
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<p class="MsoNormal">cfg.trials = find(data.trialinfo(:,1) == 64 | data.trialinfo(:,1) == 128);<o:p></o:p></p>
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<p class="MsoNormal">freq = ft_freqanalysis(cfg, data); <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">%time frequency baselined<o:p></o:p></p>
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<p class="MsoNormal">cfg=[];<o:p></o:p></p>
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<p class="MsoNormal">cfg.baseline = [-0.5 0];<o:p></o:p></p>
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<p class="MsoNormal">cfg.baselinetype = 'absolute';<o:p></o:p></p>
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<p class="MsoNormal">Base = ft_freqbaseline(cfg, freq);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">%Combine planar<o:p></o:p></p>
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<p class="MsoNormal">Comb = ft_combineplanar([],Base);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Error!<o:p></o:p></p>
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<p class="MsoNormal">Reference to non-existent field 'chanori'.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Error in ft_combineplanar (line 293)<o:p></o:p></p>
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<p class="MsoNormal"> newgrad.chanori = data.grad.chanori(sel,:);<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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