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<p class="MsoNormal"><span style="font-family:Helvetica">Hello there,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">I'm wondering about the consequence of adding "preproc" to the preprocessing parameters (e.g. using "cfg.preproc.lpfilter") versus not adding it (e.g. just using "cfg.lpfilter").
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">I first tried preprocessing my data without adding "preproc" and got this following ft_fetch_data error when I tried to visualize the data using databrowser. However, after I added "preproc" to all the
parameters, I no longer got this error and can visualize the data properly. Also, it seems like adding "preproc" changes the values in data_eeg.trial.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><img width="919" height="164" style="width:9.5729in;height:1.7083in" id="Picture_x0020_1" src="cid:image001.png@01D84A7C.FBAA6D00"></span><span style="font-family:Helvetica"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">My preprocessing steps without adding "preproc" (gave me the error when I tried to visualize data_eeg):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg <span class="apple-converted-space">
</span>= [];<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.dataset <span class="apple-converted-space">
</span>= vhdr; <span class="apple-converted-space">
</span><span class="s1">% raw data file name</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.trialfun<span class="apple-converted-space">
</span>= <span class="s2">'ft_trialfun_general'</span>;<span class="apple-converted-space">
</span><span class="s1">% selecting all trials for now</span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.trialdef.prestim</span><span class="apple-converted-space"><span style="color:black">
</span></span><span class="s3">= 0.5;</span><span class="apple-converted-space"><span style="color:black">
</span></span>% time before marker in seconds (should be generous to avoid filtering artifacts)<o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.trialdef.poststim </span><span class="apple-converted-space"><span style="color:black">
</span></span><span class="s3">= 1.5;</span><span class="apple-converted-space"><span style="color:black">
</span></span>% time after marker in seconds (should be generous to avoid filtering artifacts)<o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.trialdef.eventvalue = {</span><span class="s2">'S 12'</span><span class="s3">,
</span><span class="s2">'S 14'</span><span class="s3">, </span><span class="s2">'S 13'</span><span class="s3">,
</span><span class="s2">'S 15'</span><span class="s3">}; </span><span class="apple-converted-space"><span style="color:black">
</span></span>% markers marking stimulus events in the final test<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.trialdef.eventtype<span class="apple-converted-space">
</span>= <span class="s2">'Stimulus'</span>;<o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span>% Define trials (in cfg.trl)<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg <span class="apple-converted-space">
</span>= ft_definetrial(cfg);<span class="apple-converted-space">
</span><span class="s1">% fieldtrip function that specifies trials</span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span>% rereferencing data<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.reref <span class="apple-converted-space">
</span>= <span class="s2">'yes'</span>;<span class="apple-converted-space">
</span><span class="s1">% data will be rereferenced</span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.channel </span><span class="apple-converted-space"><span style="color:black">
</span></span><span class="s3">= setdiff(1:32, [1,12,17,32]);</span><span class="apple-converted-space"><span style="color:black">
</span></span>% in this step only for the EEG channels (including the right mastoid, elec 9)<o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.implicitref </span><span class="apple-converted-space"><span style="color:black">
</span></span><span class="s3">= </span><span class="s2">'Ref'</span><span class="s3">;</span><span class="apple-converted-space"><span style="color:black">
</span></span>% the implicit (non-recorded) reference channel is added to the data representation<o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.refchannel</span><span class="apple-converted-space"><span style="color:black">
</span></span><span class="s3">= {</span><span class="s2">'TP10'</span><span class="s3">,
</span><span class="s2">'Ref'</span><span class="s3">};</span><span class="apple-converted-space"><span style="color:black">
</span></span>% the average of these channels is used as the new reference<o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span>% filtering data<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.lpfilter<span class="apple-converted-space">
</span>= <span class="s2">'yes'</span>;<span class="apple-converted-space">
</span><span class="s1">% data will be lowpass filtered</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.lpfreq<span class="apple-converted-space">
</span>= 40; <span class="apple-converted-space">
</span><span class="s1">% lowpass frequency in Hz</span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span><span class="s3">cfg.hpfilter</span><span class="apple-converted-space"><span style="color:black">
</span></span><span class="s3">= </span><span class="s2">'no'</span><span class="s3">;
</span><span class="apple-converted-space"><span style="color:black">
</span></span>% data will NOT be highpass filtered, as this was already done online<o:p></o:p></p>
<p class="p4"><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span>% baseline correction<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>cfg.demean<span class="apple-converted-space">
</span>= <span class="s2">'yes'</span>;<span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p3"><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><span class="apple-converted-space"><span style="color:black"> </span>
</span>% apply the set parameters on the data<o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span>data_eeg <span class="apple-converted-space">
</span>= ft_preprocessing(cfg);<span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">My preprocessing steps after adding "preproc" (this did not give me error when I visualized data_eeg):
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> </span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% defining settings for trial selection<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.dataset = vhdr;
<span style="color:#028009">% raw data file name</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.trialfun =
<span style="color:#AA04F9">'ft_trialfun_general'</span>; <span style="color:#028009">
% selecting all trials for now</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.trialdef.prestim = 0.5;
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% time before marker in seconds (should be generous to avoid filtering artifacts)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.trialdef.poststim = 1.5;
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% time after marker in seconds (should be generous to avoid filtering artifacts)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.trialdef.eventvalue = {</span><span style="font-size:7.5pt;font-family:Courier;color:#AA04F9">'S 12'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,
</span><span style="font-size:7.5pt;font-family:Courier;color:#AA04F9">'S 14'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,
</span><span style="font-size:7.5pt;font-family:Courier;color:#AA04F9">'S 13'</span><span style="font-size:7.5pt;font-family:Courier;color:black">,
</span><span style="font-size:7.5pt;font-family:Courier;color:#AA04F9">'S 15'</span><span style="font-size:7.5pt;font-family:Courier;color:black">};
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% markers marking stimulus events in the final test<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.trialdef.eventtype =
<span style="color:#AA04F9">'Stimulus'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% Define trials (in cfg.trl)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg = ft_definetrial(cfg);
<span style="color:#028009">% fieldtrip function that specifies trials</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% rereferencing data<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.preproc.reref =
<span style="color:#AA04F9">'yes'</span>; <span style="color:#028009">
% data will be rereferenced</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.channel = setdiff(1:32, [1,12,17,32]);
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% in this step only for the EEG channels (including the right mastoid, elec 9)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black"> cfg.preproc.implicitref =
</span><span style="font-size:7.5pt;font-family:Courier;color:#AA04F9">'Ref'</span><span style="font-size:7.5pt;font-family:Courier;color:black">;
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% the implicit (non-recorded) reference channel is added to the data representation<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.preproc.refchannel = {<span style="color:#AA04F9">'TP10'</span>,
<span style="color:#AA04F9">'Ref'</span>}; <span style="color:#028009">
% the average of these channels is used as the new reference</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% filtering data<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.preproc.lpfilter =
<span style="color:#AA04F9">'yes'</span>; <span style="color:#028009">
% data will be lowpass filtered</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.preproc.lpfreq = 40;
<span style="color:#028009">% lowpass frequency in Hz</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.preproc.hpfilter =
<span style="color:#AA04F9">'no'</span>; <span style="color:#028009">
% data will NOT be highpass filtered, as this was already done online</span><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:#028009"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% baseline correction<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> cfg.preproc.demean =
<span style="color:#AA04F9">'yes'</span>;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">%cfg.baselinewindow = [-0.2 0]; % no baseline correction necessary<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier;color:black">
</span><span style="font-size:7.5pt;font-family:Courier;color:#028009">% apply the set parameters on the data<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.5pt;font-family:Courier"> data_eeg = ft_preprocessing(cfg); <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Could you let me know why this might be the case?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Thank you!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:Helvetica">Anqi<o:p></o:p></span></p>
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