<div dir="ltr"><div class="gmail_default" style="font-size:small">Dear Florian,</div><div class="gmail_default" style="font-size:small">You are not clear about your actual sample rate:</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">> I do not know either how much trust I have to put in that warning and correction of the sampling rate in the first place.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Clearly, you should know your own sampling rate from the Neurolynx acquisition software.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">It would seem this is the primary thing you need to resolve.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Regards,</div><div class="gmail_default" style="font-size:small">Per</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"> </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div><div dir="ltr"><div><div><div dir="ltr"><div><b><br></b></div><div><b>Per M Knutsen</b></div><div><font size="1">University of Oslo</font></div><div><font size="1">Dept. of Molecular Medicine, Physiology Sect.</font></div><div><font size="1">PB 1103 Blindern, NO-0317 Oslo</font></div><div><font color="#1155cc" size="1"><a href="tel:%2B47.45103762" value="+4745103762" target="_blank">+47.45103762</a></font></div></div></div></div><div dir="ltr"><div style="font-size:small"></div></div></div></div></div><div dir="ltr"><div style="font-size:small"></div></div></div></div></div>
<br><div class="gmail_quote">On Sat, Oct 15, 2016 at 9:25 AM, Florian Gerard-Mercier <span dir="ltr"><<a href="mailto:florian@brain.riken.jp" target="_blank">florian@brain.riken.jp</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear all,<div><br></div><div>I am wondering, was my question unclear, or maybe no one is using Neuralynx data?</div><div>I can think of ways to avoid these two problems, but I would prefer to find a proper solution if possible. </div><div><br></div><div>Thanks in advance,</div><div><br><div>
<span class="m_-3099422565437113932Apple-style-span" style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>Florian Gerard-Mercier</div><div><br></div></span><br class="m_-3099422565437113932Apple-interchange-newline">
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<br><div><blockquote type="cite"><div>On 14 Oct, 2016, at 3:08 PM, Florian Gerard-Mercier <<a href="mailto:florian@brain.riken.jp" target="_blank">florian@brain.riken.jp</a>> wrote:</div><br class="m_-3099422565437113932Apple-interchange-newline"><div><div style="word-wrap:break-word">Dear community,<div><br></div><div><br></div><div>My name is Florian Gerard-Mercier and I work in Keiji Tanaka’s laboratory in Riken BSI, Japan.</div><div><br></div><div><br></div><div>I am new to Fieldtrip.</div><div>My goal is to do a simple analysis of ECoG data in response to electrical stimulation (all in monkey cortex). To this effect I followed the TMS-EEG tutorial (since the issues are almost identical).</div><div>The recording system is Neuralynx.</div><div><br></div><div>I have encountered 2 problems which I don’t believe are related.</div><div>I have basically followed the tutorials to the letter so except if I mention otherwise, the cfg, etc. are standard.</div><div><br></div><div><u><b>1) Fsample discrepancy between data and header.</b></u></div><div>When I load Neuralynx data, I get warnings that the sample rate is actually half that in the header, and is thus being corrected (note, 16129 instead of 32258Hz).</div><div>This is no problem, until I get the final results where I noticed that my 50Hz noise is now represented as lasting 40ms for each cycle (= twice longer than it actually is).</div><div>Navigating in the workspace, I noticed that even though cfg.Fs is 16129 as expected, somehow the data outputted by ft_preprocessing has a field fsample equal to half that number (8064.5).</div><div>This later gives many conflicts such as: if I force data.fsample to be 16129, I have the correct time axis in the end, but now my trial duration is only half that which I want…</div><div>Any idea on how to solve this issue? I haven’t found any previous ticket on this Fsample discrepancy issue.</div><div>I do not know either how much trust I have to put in that warning and correction of the sampling rate in the first place.</div><div><br></div><div><u><b>2) 50Hz line noise filtering</b></u></div><div>The previous point makes it so that if I filter 50Hz, of course nothing happens. But even if I filter 25Hz (or 50Hz with the Fsample corrected back to 16129), the attenuation is far too small (whether I use padding or not). I did look up the similar problems that had been submitted to this list in the past, but didn’t find any satisfactory fix.</div><div>To give an idea:</div><div><div>cfg = [];</div><div>cfg.Fsample = 1000; % I downsampled the data in the meantime as said in the tuto</div><div>cfg.bsfilter = 'yes';</div><div>cfg.bsfiltord = 2; % somehow I have an error that the filtering doesn’t work every time I try to run it with an order >2</div><div>cfg.bsfreq = [49.9 50.1];</div><div>filtDat = ft_preprocessing(cfg, data_lite);</div><div><br></div><div><div>cfgbrowse = []; cfgbrowse.viewmode = 'butterfly';</div><div>ft_databrowser(cfgbrowse, dat_lite /// filtDat); % screenshots of both below</div></div><div><br></div><div>changes this</div><div><span id="m_-3099422565437113932cid:A61F9FBF-4C22-4418-BF33-2A7E0474BE79@bnf.brain.riken.jp"><data_lite.jpeg></span></div><div><br></div><div>into that</div><div><br></div><div><span id="m_-3099422565437113932cid:D9CEB025-4841-41D7-AEA6-DB89088A2C37@bnf.brain.riken.jp"><filtDat.jpeg></span></div><div><br class="m_-3099422565437113932webkit-block-placeholder"></div><div>{Note also the issue with Fsample: here I have a time axis that corresponds to my 50Hz noise, but the duration of the trial is reduced from [-0.05, 0.45] by a factor of 2.}</div><div><br></div><div>This is in stark contrast to what happens if I use the bandstop filter directly on the raw data:</div><div><div style="margin:0px;line-height:normal">dat = ft_read_data(dataset_dir);</div></div><div><div style="margin:0px;line-height:normal">dat_filt = ft_preproc_bandstopfilter(dat, 16129, [49.9 50.1], 2);</div></div><div>changes this</div><div><span id="m_-3099422565437113932cid:4FF67112-09FC-4A3B-A444-C64EB817293E@bnf.brain.riken.jp"><RawData.jpeg></span></div><div><br></div><div>into that</div><div><br></div><div><span id="m_-3099422565437113932cid:DAD0B9D2-A389-4AC0-AF4F-D22BC8CC53AF@bnf.brain.riken.jp"><RawData_after_filter.jpeg></span></div><div><br></div><div>Which should be perfect for my simple purposes. (Here I just did a simple Matlab plot, so the x axis numbering is not actual time)</div><div><br></div><div>Of course, I tried to feed that filtered data into the preprocessing pipeline by doing </div><div><div style="margin:0px;line-height:normal">cfg = ft_rejectartifact(cfg_<wbr>artifact); %cfg_artifact is defined as in the tutorial, it is to reject the electrical stimulation artifacts. The problem should not stem from here.</div></div><div><div style="margin:0px;line-height:normal">data_artifact_rejected = ft_preprocessing(cfg, dat_filt);</div></div><div>But I get the error that dat_filt is not raw or comp data.</div><div><br></div><div>I have read that it is recommended to do the line noise filtering after the trial segmentation and stimulation artefact removal, but 1) it doesn’t seem to work well, 2) I don’t really understand why, given that my artefacts are nowhere near the 50Hz frequency.</div><div><br></div><div>So for this point:</div><div>- how to make the (recommended) 50Hz post processing work?</div><div>- or more simply, how could I feed prefiltered data to ft_preprocessing?</div><div><br></div><div><br></div><div><br></div><div><br></div><div>Thank you very much for your consideration and I look forward to your help.</div><div><br></div><div>All the best,</div><div><br></div><div><br></div><div>
<span class="m_-3099422565437113932Apple-style-span" style="border-collapse:separate;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-alternates:normal;font-variant-east-asian:normal;line-height:normal;border-spacing:0px"><div>Florian</div></span>
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