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Pramod,
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<div class="">I don’t understand how ‘combining all the three blocks before the preprocessing’ would help you to preserve the channel positions. Apparently, these are different for each of the blocks in your case. It’s also not clear to me, why this is causes
problem in your specific case. </div>
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<div class="">Anyway, ft_appenddata throws the grad-field away, since it recognizes that the channel (and coil) positions are different in each of the runs.</div>
<div class="">If you still want to obtain some kind of ‘average’ representation of the channel position, you can use ft_average_sens. If the positions are not altogether too different, it might be OK to average the positions across blocks, although technically
it’s of course incorrect to do so. Yet, if for each of the blocks you have applied block-specific spatial transformations (e.g. maxfilter) then it’s a different story altogether, and things will become hairy very rapidly.</div>
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<div class="">Best wishes,</div>
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<div class="">Jan-Mathijs</div>
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<blockquote type="cite" class="">
<div class="">On 19 Nov 2018, at 19:19, Gaur, Pramod <<a href="mailto:p.gaur@ulster.ac.uk" class="">p.gaur@ulster.ac.uk</a>> wrote:</div>
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Dear Team,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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I have a quick concern, I have a cognitive task and recorded three blocks. Is there any way in which I can combine all the three blocks before the preprocessing. I have alternate to preprocess the blocks separately and then combining them. In this case, I lose
the<span class="Apple-converted-space"> </span><span style="font-size: 10pt; font-family: 'Courier New';" class="">data_MEG_filt .</span>grad.chanpos location.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">cfg = [];</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.dataset = filename;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% % cfg = ft_definetrial(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.trialdef.eventtype =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'STI101'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%cfg.trialdef.eventtype = 'gui';</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.trialdef.eventvalue = [16 17 18 32 33 34]</span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% 17 18];% put your own</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.trialdef.prestim = prestim;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.trialdef.poststim = poststim;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.length = 1;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg = ft_definetrial(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> </span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> </span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% read in the data from the magnetometer</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.channel = {'MEGMAG','STI101'};</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.channel = {</span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'MEG'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">};</span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">%,'-MEG2331','-MEG0122'};%%{'MEG*2','MEG*3'};%selected_sensors;%{'MEG'};%</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.lpfilter = 'yes';</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.lpfreq = 40;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.hpfilter = 'yes';</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.hpfreq = 1;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.continuous =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.detrend =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'no'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.demean =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.dftfilter =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'yes'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> <span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class="">% cfg.dftfreq =[50 100 150];% power
line noise</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.bpfreq = [1 48];</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.metric =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'zvalue'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.layout =<span class="Apple-converted-space"> </span></span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'neuromag306all.lay'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> cfg.baselinewindow = [-0.5 0];</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> data_MEG_filt = ft_preprocessing(cfg);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class=""> </span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> if isempty(data_MEG_filt)</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> data_MEG_filt=data;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> grad = data.grad;</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> else</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> cfg = [];</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> data_MEG_filt = ft_appenddata(cfg, data_MEG_filt,data);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New'; color: forestgreen;" class=""> end</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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Any advice will be highly appreciated.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 10pt; font-family: Arial, sans-serif;" class=""><o:p class=""> </o:p></span></div>
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<span class=""><span id="cid:image001.jpg@01D48034.5FFF0430"><image001.jpg></span><o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10.5pt; font-family: Arial, sans-serif; color: rgb(26, 42, 79);" class="">Dr Pramod Gaur<o:p class=""></o:p></span></b></p>
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<span style="font-size: 10pt; font-family: Arial, sans-serif;" class="">Research Assistant in Neuro-Imaging Technology<o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(187, 164, 97);" class="">E:</span></b><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(74, 74, 73);" class=""> <a href="mailto:p.gaur@ulster.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">p.gaur@ulster.ac.uk</a><span class="Apple-converted-space"> </span> </span><b class=""><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(187, 164, 97);" class="">W:</span></b><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(74, 74, 73);" class=""> </span><span style="font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><a href="http://www.ulster.ac.uk/" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Arial, sans-serif;" class="">www.ulster.ac.uk</span></a></span><span style="font-size: 9pt; font-family: Arial, sans-serif; color: rgb(74, 74, 73);" class=""><o:p class=""></o:p></span></p>
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</font><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></div>
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