<div dir="ltr"><img width="0" height="0" class="mailtrack-img" alt="" style="display:flex" src="https://mailtrack.io/trace/mail/afee622279f3f5cc4ac1c2b8be056d6f28911fed.png?u=648108">Hi all,<div><br></div><div>One more small problem to get fixed. When I apply a low-pass or high-pass filter, SOME event ids are not detected. Tested with the code I specified in the thread with linked data.</div><div><br></div><div>Any possible reasons?</div><div><br></div><div>Thank you,</div><div><br></div><div>Senaka</div><div><br></div><div><br><br><br><br><div style="display:inline">
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</div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jul 10, 2017 at 6:05 PM, Senaka Amarakeerthi <span dir="ltr"><<a href="mailto:senakahks@gmail.com" target="_blank">senakahks@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><img width="0" height="0" class="m_6878667097584448860mailtrack-img" alt="" src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7">Hi Jaakko and Alex, <div><br></div><div>Thanks a lot. Finally, Jaakko's trick worked.</div><div><br></div><div>This is the plot.</div><div><br></div><div><a href="https://ibb.co/eKt6Pa" target="_blank">https://ibb.co/eKt6Pa</a></div><div><br></div><div>Thank you again for spending your valuable to get the code fixed up.</div><span class=""><div><br></div><div>Senaka<br><br><br><br><div style="display:inline">
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</div></div></div></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jul 10, 2017 at 4:04 PM, Jaakko Leppakangas <span dir="ltr"><<a href="mailto:jaeilepp@gmail.com" target="_blank">jaeilepp@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">You can do<div><br></div><div>import mne</div><div>mne.sys_info()</div><div><br></div><div>I think you can also work around the issue by doing </div><div>raw.set_channel_types({'MARKER<wbr>': 'stim'})<br></div><div><br></div><div>after constructing the RawArray. The amplitude of the stimulus channel is messing up the plot.</div><span class="m_6878667097584448860HOEnZb"><font color="#888888"><div><br></div><div>-Jaakko</div></font></span></div><div class="m_6878667097584448860HOEnZb"><div class="m_6878667097584448860h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jul 10, 2017 at 11:52 AM, Senaka Amarakeerthi <span dir="ltr"><<a href="mailto:senakahks@gmail.com" target="_blank">senakahks@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><img width="0" height="0" class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787mailtrack-img" alt="" src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7">Dear Jaakko,<div><br></div><div>I issued the following command</div><div>pip install mne --upgrade<br></div><div><br></div><div>Result:<br>Requirement already up-to-date: mne in ./mne-python</div><div><p class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-p1">Is there a direct command to check the version?</p><p class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-p1">I use python 2.7 and macOS Sierra.</p><p class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-p1"><br></p><p class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-p1">Thanks</p><p class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-p1">Senaka</p><p class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-p1"><span class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail-s1"><br></span></p></div><div><br><br><br><br><div style="display:inline">
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</div></div></div></div><div class="gmail_extra"><div><div class="m_6878667097584448860m_-3350889800022295183h5"><br><div class="gmail_quote">On Mon, Jul 10, 2017 at 11:19 AM, Jaakko Leppakangas <span dir="ltr"><<a href="mailto:jaeilepp@gmail.com" target="_blank">jaeilepp@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I was able to reproduce the plot with version 0.13. I'm not sure what's the cause of it, but in v. 0.14 it looks better. Can you try updating mne to the latest version?<span class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787HOEnZb"><font color="#888888"><div><br></div><div>-Jaakko</div></font></span></div><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787HOEnZb"><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Jul 9, 2017 at 2:22 PM, Senaka Amarakeerthi <span dir="ltr"><<a href="mailto:senakahks@gmail.com" target="_blank">senakahks@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><img width="0" height="0" class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303m_5330854017795098904mailtrack-img" alt="" src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7">Hi,<div><br></div><div>I am migrating from EEGLAB and tried to apply baseline corrections and filters, unfortunately, those attempts ended up with another set of errors. Highly appreciating somebody's support since I am exhausted. </div><div><br></div><div>Sample file URL:</div><div><a href="https://www.dropbox.com/s/vwvy4duwkahysfk/ChinthakaDahnushka.edf?dl=0" target="_blank">https://www.dropbox.com/s/vwvy<wbr>4duwkahysfk/ChinthakaDahnushka<wbr>.edf?dl=0</a><br></div><div><br></div><div>The code so far I used:</div><div><br></div><div><pre style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt"><span style="color:rgb(0,0,128);font-weight:bold">import </span>mne<br><span style="color:rgb(0,0,128);font-weight:bold">import </span>numpy <span style="color:rgb(0,0,128);font-weight:bold">as </span>np<br><span style="color:rgb(0,0,128);font-weight:bold">import </span>matplotlib.pyplot <span style="color:rgb(0,0,128);font-weight:bold">as </span>plt<br><br><br>raw = mne.io.read_raw_edf(<span style="color:rgb(0,128,0);font-weight:bold">'Chinthaka<wbr>Dahnushka.edf'</span>, <span style="color:rgb(102,0,153)">preload</span>=<span style="color:rgb(0,0,128)">True</span>)<br>raw = raw.drop_channels([<span style="color:rgb(0,128,0);font-weight:bold">'COUNTER'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'INTERPOLATED'</span>,<span style="color:rgb(0,128,0);font-weight:bold">'RAW_CQ'</span>,<span style="color:rgb(0,128,0);font-weight:bold">'GYROX<wbr>'</span>,<span style="color:rgb(0,128,0);font-weight:bold">'GYROY'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'SYNC'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'TIME_STAMP_s'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'TIME_STAMP_ms'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_AF3'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_F7'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_F3'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_FC5'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_T7'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_P7'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_O1'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_O2'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_P8'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_T8'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_FC6'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_F4'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_F8'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_AF4'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'CQ_CMS'</span>, <span style="color:rgb(0,128,0);font-weight:bold">'STI 014'</span>])<span><br><br>data = raw[:, :][<span style="color:rgb(0,0,255)">0</span>]<br><br>data[<span style="color:rgb(0,0,255)">14</span>] *= <span style="color:rgb(0,0,255)">1000000<br></span><span style="color:rgb(0,0,255)"><br></span>raw = mne.io.RawArray(data, <a href="http://raw.info" target="_blank">raw.info</a>)<br><br>events = mne.find_events(raw, <span style="color:rgb(102,0,153)">stim_channel</span>=<span style="color:rgb(0,128,0);font-weight:bold">'MARKER'</span>)<br><br><br></span><span><span style="color:rgb(0,0,128);font-weight:bold">print</span>(<span style="color:rgb(0,128,0);font-weight:bold">'Found %s events, first five:' </span>% <span style="color:rgb(0,0,128)">len</span>(events))<br></span><span style="color:rgb(0,0,128);font-weight:bold">print</span>(events[:<span style="color:rgb(0,0,255)">5</span>])<br><br><br>event_id = {<span style="color:rgb(0,128,0);font-weight:bold">'two'</span>: <span style="color:rgb(0,0,255)">2</span>}<br><br>epochs = mne.Epochs(raw, events, <span style="color:rgb(102,0,153)">event_id</span>=event_id, <span style="color:rgb(102,0,153)">tmin</span>=-<span style="color:rgb(0,0,255)">0.2</span>, <span style="color:rgb(102,0,153)">tmax</span>=<span style="color:rgb(0,0,255)">1.5</span>)<br><br><br>epochs_data = epochs[<span style="color:rgb(0,128,0);font-weight:bold">'two'</span>].get_data()<br><br><span style="color:rgb(128,128,128);font-style:italic"><br></span><span style="color:rgb(0,0,128);font-weight:bold">print</span>(epochs_data.shape)<br><br><br>epochs.plot(<span style="color:rgb(102,0,153)">block</span>=<span style="color:rgb(0,0,128)">True</span>)<br></pre><pre style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt"><br></pre><pre style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt">This is the plot I ended up with </pre></div><div><a href="https://ibb.co/ccKXvF" style="font-size:12.8px" target="_blank">https://ibb.co/ccKXvF</a></div><span><div><br></div><div>Thanks,</div><div><br></div><div>Senaka<br><br><br><br><div style="display:inline">
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</div></div></div></span><div><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Jul 9, 2017 at 1:33 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-pa<wbr>ristech.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">hi,<div><br></div><div>did you baseline correct your Epochs or high pass filter the raw data?</div><div>if not please do.</div><div><br></div><div>you may have a big offset in the values.</div><div><br></div><div>HTH,</div><div>Alex</div></div><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303m_5330854017795098904HOEnZb"><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303m_5330854017795098904h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Jul 8, 2017 at 4:38 PM, Senaka Amarakeerthi <span dir="ltr"><<a href="mailto:senakahks@gmail.com" target="_blank">senakahks@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><img width="0" height="0" class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303m_5330854017795098904mailtrack-img" alt="" src="data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7">Hi Alex,<div><br></div><div>Thank you for your time. You can check screenshots of the graphs below, which were not available in the last post.</div><div><br></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt;white-space:pre-wrap"><br></span></div><div><span style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt;white-space:pre-wrap">raw</span><span style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt;white-space:pre-wrap">.plot(</span><span style="font-family:Menlo;font-size:9pt;white-space:pre-wrap;color:rgb(102,0,153)">block</span><span style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt;white-space:pre-wrap">=</span><span style="font-family:Menlo;font-size:9pt;white-space:pre-wrap;color:rgb(0,0,128)">True</span><span style="color:rgb(0,0,0);font-family:Menlo;font-size:9pt;white-space:pre-wrap">)</span><br></div><div><a href="https://ibb.co/n6GeaF" target="_blank">https://ibb.co/n6GeaF</a><br></div><div><br></div><div><pre style="white-space:pre-wrap;color:rgb(0,0,0);font-family:Menlo;font-size:9pt">epochs<span style="font-size:9pt">.plot(</span><span style="font-size:9pt;color:rgb(102,0,153)">block</span><span style="font-size:9pt">=</span><span style="font-size:9pt;color:rgb(0,0,128)">True</span><span style="font-size:9pt">)</span></pre></div><div><a href="https://ibb.co/ccKXvF" target="_blank">https://ibb.co/ccKXvF</a><br></div><div><br></div><div><br>So, I guess this is not a problem with an amplitude of the signal. Am I correct?</div><div><br></div><div>Thanks,</div><span><div><br></div><div>Senaka<br><br><br><div style="display:inline">
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</div></div></div></span><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303m_5330854017795098904m_157829887483510462h5">On Sat, Jul 8, 2017 at 7:49 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-pa<wbr>ristech.fr</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787m_7336481911137255303m_5330854017795098904m_157829887483510462h5"><div dir="ltr"><div class="gmail_extra">I don't see any problem. Make sure your data are in Volts not micro-Volts.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Best,</div><div class="gmail_extra">Alex</div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div></div></div><span class="m_6878667097584448860m_-3350889800022295183HOEnZb"><font color="#888888">-- <br><div class="m_6878667097584448860m_-3350889800022295183m_-7782792980571659787gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Senaka Amarakeerthi, PhD(Japan<wbr>)</div><div>Senior Lecturer in Computer Science<br>Faculty of Technology<br>University of Sri Jayewardenepura</div><div>Nugegoda<br>Sri Lanka<br>email: <a href="mailto:senaka@sjp.ac.lk" target="_blank">senaka@sjp.ac.lk</a></div><div>Mobile: <a href="tel:+94%2071%20204%203212" value="+94712043212" target="_blank">+(94)-71-2043212</a></div><div>Office: <span style="font-size:12.8px">+(94)-</span>11-2802969</div></div></div></div></div></div></div></div></div></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="m_6878667097584448860gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Senaka Amarakeerthi, PhD(<wbr>Japan)</div><div>Senior Lecturer in Computer Science<br>Faculty of Technology<br>University of Sri Jayewardenepura</div><div>Nugegoda<br>Sri Lanka<br>email: <a href="mailto:senaka@sjp.ac.lk" target="_blank">senaka@sjp.ac.lk</a></div><div>Mobile: <a href="tel:071%20204%203212" value="+94712043212" target="_blank">+(94)-71-2043212</a></div><div>Office: <span style="font-size:12.8px">+(94)-</span>11-2802969</div></div></div></div></div></div></div></div></div></div></div>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Senaka Amarakeerthi, PhD(Japan)</div><div>Senior Lecturer in Computer Science<br>Faculty of Technology<br>University of Sri Jayewardenepura</div><div>Nugegoda<br>Sri Lanka<br>email: <a href="mailto:senaka@sjp.ac.lk" target="_blank">senaka@sjp.ac.lk</a></div><div>Mobile: +(94)-71-2043212</div><div>Office: <span style="font-size:12.8px">+(94)-</span>11-2802969</div></div></div></div></div></div></div></div></div></div></div>
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