<div dir="ltr">Dear Edwige,<div><br></div><div>Thank you Edwige for clear explanation.</div><div><br></div><div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">> 1) For participant 9, ICA was not successful and during running ICA it only got until step one where I got the error message. Therefore, there is no information about the variable icasphere.</div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">Good to discover the problem. Check what was wrong and confirm if ICA can be performed successfully.</div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">> 2) With your suggestion, I checked again for all my participants whether nbchan and icasphere are the same, I discovered that for the ones that I did not exclude the eye electrode before ICA and where I clicked on the '...channel' thing, I got ICA where the number of channels is NOT equal to icasphere. Do you think I should run ICA again for these participants where number of channels is NOT equal to icasphere? </div><br></div><div>Yes, you should run ICA again to see if it works.</div><div>If ICA takes too long time, you can specify the ICA iteration number by using 'maxsteps', 20 to stop at 20th iteration for example.</div><div><br></div><div>Looks like the problem is almost solved. Looking forward to good news!</div><div><br></div><div>Makoto</div><div><br></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Jul 12, 2018 at 1:41 AM Sijyeniyo, E. <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Makoto, <div><br></div><div>Here is the output I get if I type "EEG" for this particular participant (participant 9):</div><div><br></div><div><div>EEG = </div><div><br></div><div> struct with fields:</div><div><br></div><div> setname: 'SPES_cleanwithouteyes_[pp0009] '</div><div> filename: '9_SPES_cleanwithouteyes_[pp0009].set'</div><div> filepath: 'C:\Users\p281582\Documents\Data that needs ICA again\'</div><div> subject: ''</div><div> group: ''</div><div> condition: ''</div><div> session: []</div><div> comments: 'Original file: SPES0009.eeg'</div><div> nbchan: 55</div><div> trials: 1</div><div> pnts: 653307</div><div> srate: 250</div><div> xmin: 0</div><div> xmax: 2.6132e+03</div><div> times: [1×653307 double]</div><div> data: [55×653307 double]</div><div> icaact: []</div><div> icawinv: []</div><div> icasphere: []</div><div> icaweights: []</div><div> icachansind: []</div><div> chanlocs: [1×55 struct]</div><div> urchanlocs: []</div><div> chaninfo: [1×1 struct]</div><div> ref: 'averef'</div><div> event: [1×1916 struct]</div><div> urevent: [1×1922 struct]</div><div> eventdescription: {'' '' '' '' '' '' '' ''}</div><div> epoch: []</div><div> epochdescription: {}</div><div> reject: [1×1 struct]</div><div> stats: [1×1 struct]</div><div> specdata: []</div><div> specicaact: []</div><div> splinefile: ''</div><div> icasplinefile: ''</div><div> dipfit: []</div><div> history: '↵EEG.etc.eeglabvers = '14.1.2'; % this tracks which version of EEGLAB is being used, you may ignore it↵EEG = </div><div> saved: 'yes'</div><div> etc: [1×1 struct]</div><div> datfile: '9_SPES_cleanwithouteyes_[pp0009].fdt'</div></div><div><br></div><div><br></div><div>As you can see, there is no information about icasphere, most likely because ICA never successfully ran for this participant. When I started ICA, it started lowering the learning rate and then getting only to step one and then I got the error message, so the ICA was never completed. </div><div><br></div><div>However, your suggestion has made me realise that I might have made a mistake for some other participants. </div><div><br></div><div>Initially I ran my participants in the following way: </div><div>
<span style="color:rgb(80,0,80);text-decoration-style:initial;text-decoration-color:initial;font-family:Arial;font-size:11pt;text-align:justify;white-space:pre-wrap;background-color:rgb(255,255,255);font-variant-east-asian:normal;vertical-align:baseline"><br class="m_-3323439657313735903m_4635028319333169514gmail-Apple-interchange-newline">> Click on the button </span><span style="color:rgb(80,0,80);text-decoration-style:initial;text-decoration-color:initial;font-family:Arial;font-size:11pt;text-align:justify;white-space:pre-wrap;background-color:rgb(255,255,255);font-style:italic;font-variant-east-asian:normal;vertical-align:baseline">... <font color="#0000ff">channels</font></span><span style="color:rgb(80,0,80);text-decoration-style:initial;text-decoration-color:initial;font-family:Arial;font-size:11pt;text-align:justify;white-space:pre-wrap;background-color:rgb(255,255,255);font-variant-east-asian:normal;vertical-align:baseline"><font color="#0000ff"> to select all the channels except EOGh and EOGvl</font>. The eye electrodes need to be excluded, because they don’t have the same reference as the other electrodes in our dataset. The eye electrodes are bipolar, meaning that they are referenced to each other. The other electrodes, however, are referenced to the average of all electrodes.</span>
<br></div><div><br></div><div>However, you advised me not to click on the '...channel' things as this might cause some errors. You suggested that I should remove the eye electrodes before running ICA and therefore I did not have to click on the '...channels' thing. After this advice, I started rejecting my eye electrodes before ICA, but for my first participants, I did not. But for these first participants, ICA was still successful. Now I am looking back at those ICAs and I have discovered that: </div><div><br></div><div>
<ol style="font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><li style="margin-left:15px">The number of channels (EEG.nbchan)</li><li style="margin-left:15px">The number of rows in EEG.icasphere<span> </span><u>right after</u><span> </span>ICA</li></ol>
....are NOT the same. For instance, for this participant (participant 7) 'EEG' gives the following output: </div><div><br></div><div><div>EEG = </div><div><br></div><div> struct with fields:</div><div><br></div><div> setname: 'SPES_clean_ica_[pp0007]'</div><div> filename: '7_SPES_icacomplete_[pp0007].set'</div><div> filepath: 'C:\Users\p281582\Documents\Preprocessing_UPDATED\'</div><div> subject: ''</div><div> group: ''</div><div> condition: ''</div><div> session: []</div><div> comments: 'Original file: SPES0007.eeg'</div><div> <font color="#ff0000"> nbchan: 60</font></div><div> trials: 1</div><div> pnts: 640153</div><div> srate: 250</div><div> xmin: 0</div><div> xmax: 2.5606e+03</div><div> times: [1×640153 double]</div><div> data: [60×640153 double]</div><div> icaact: [57×640153 double]</div><div> icawinv: [58×57 double]</div><div> <font color="#ff0000"> icasphere:<span style="background-color:rgb(255,255,255)"> [58×58 double]</span></font></div><div> icaweights: [57×58 double]</div><div> icachansind: [1×58 double]</div><div> chanlocs: [1×60 struct]</div><div> urchanlocs: []</div><div> chaninfo: [1×1 struct]</div><div> ref: 'averef'</div><div> event: [1×1853 struct]</div><div> urevent: [1×1922 struct]</div><div> eventdescription: {'' '' '' '' '' '' '' ''}</div><div> epoch: []</div><div> epochdescription: {}</div><div> reject: [1×1 struct]</div><div> stats: [1×1 struct]</div><div> specdata: []</div><div> specicaact: []</div><div> splinefile: ''</div><div> icasplinefile: ''</div><div> dipfit: []</div><div> history: '↵EEG.etc.eeglabvers = '14.1.2'; % this tracks which version of EEGLAB is being used, you may ignore it↵EEG = </div><div> saved: 'yes'</div><div> etc: [1×1 struct]</div><div> datfile: '7_SPES_icacomplete_[pp0007].fdt'</div></div><div><br></div><div>As you can see, nbchan = 60 but icasphere is 58 (i.e., the second dimension of the n x m matrix; m IS NOT the same as the number of channels).</div><div><br></div><div>So do you think I should run ICA again for these participants where the two variables nbchan and icasphere are not the same?</div><div><br></div><div>To summarize. I have two issues: </div><div>1) For participant 9, ICA was not successful and during running ICA it only got until step one where I got the error message. Therefore, there is no information about the variable icasphere.</div><div>2) With your suggestion, I checked again for all my participants whether nbchan and icasphere are the same, I discovered that for the ones that I did not exclude the eye electrode before ICA and where I clicked on the '...channel' thing, I got ICA where the number of channels is NOT equal to icasphere. Do you think I should run ICA again for these participants where number of channels is NOT equal to icasphere? </div><div><br></div><div>Hopefully you can still follow the story here, if you have any questions about what I mean, please ask them. I tried to explain it as clear as possible but it's sometimes hard to do so via email. </div><div><br></div><div>Thanks again Makoto, you are a great help with all of this!</div><div><br></div><div>Best,</div><div>Edwige</div><div><br></div><div><br><div class="m_-3323439657313735903m_4635028319333169514gmail-yj6qo m_-3323439657313735903m_4635028319333169514gmail-ajU" style="outline:none;padding:10px 0px;width:22px;margin:2px 0px 0px;font-size:12.8px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><div id="m_-3323439657313735903m_4635028319333169514gmail-:vf" class="m_-3323439657313735903m_4635028319333169514gmail-ajR" style="background-color:rgb(241,241,241);border:1px solid rgb(221,221,221);clear:both;line-height:6px;outline:none;width:20px"><img class="m_-3323439657313735903m_4635028319333169514gmail-ajT" src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif" style="background:url("") no-repeat;height:8px;opacity:0.3;width:20px"></div></div>
</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 11, 2018 at 8:35 PM, Makoto Miyakoshi <span dir="ltr"><<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</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">Dear Edwige,<span><div><br></div><div><span style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">> I have no idea what this means and at this point I am quite desperate because I really need this participant…</span><br></div><div><br></div></span><div>Don't worry Edwige, this data will be fine.</div><div>In the worst case, you can still send it to me for re-processing.</div><div><br></div><div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span><div>> 1: the number of channels is: 55</div><div><br></div></span><div>Ok it means you do have 55 channels.</div><div><br></div></div><span><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">> 2: the number of rows is I think: 53 (?) </div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div></span><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">Sorry, I should have asked you to do it in this way: Could you please copy and paste all the output from typing 'EEG'? It's like this.</div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><div>EEG = </div><div><br></div><div> setname: '5022'</div><div> filename: '5022.set'</div><div> filepath: '/data/data/data/data/data/data/data'</div><div> subject: '5022'</div><div> group: ''</div><div> condition: ''</div><div> session: []</div><div> comments: ''</div><div> nbchan: 128</div><div> trials: 1</div><div> pnts: 540914</div><div> srate: 250</div><div> xmin: 0</div><div> xmax: 2.1637e+03</div><div> times: [1x540914 double]</div><div> <font color="#ff0000">data: [128x540914 single]</font></div><div> icaact: [123x540914 single]</div><div> icawinv: [128x123 double]</div><div> <font color="#ff0000">icasphere: [123x128 double]</font></div><div> icaweights: [123x123 double]</div><div> icachansind: [1x128 double]</div><div> chanlocs: [1x128 struct]</div><div> urchanlocs: []</div><div> chaninfo: [1x1 struct]</div><div> ref: 'averef'</div><div> event: [1x1096 struct]</div><div> urevent: [1x1015 struct]</div><div> eventdescription: {'' '' '' ''}</div><div> epoch: []</div><div> epochdescription: {}</div><div> reject: [1x1 struct]</div><div> stats: [1x1 struct]</div><div> specdata: []</div><div> specicaact: []</div><div> splinefile: ''</div><div> icasplinefile: ''</div><div> dipfit: [1x1 struct]</div><div> history: [1x432 char]</div><div> saved: 'yes'</div><div> etc: [1x1 struct]</div><div> datfile: '5022.fdt'</div><div><br></div><div><br></div></div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">I made a mistake, I should have asked to tell me the number of columns instead of rows (i.e., the second dimension of the n x m matrix; m must be the same as the number of channels).</div><span class="m_-3323439657313735903m_4635028319333169514HOEnZb"><font color="#888888"><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div style="font-size:small;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial">Makoto</div></font></span></div><div><div class="m_-3323439657313735903m_4635028319333169514h5"><div><br></div><div><br></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jul 10, 2018 at 1:56 AM E. Sijyeniyo <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Dear Makoto, <div><br></div><div>I have been spending some time now trying to figure out what your suggestion means, but I am afraid I don’t really understand what you mean. </div><div><br></div><div>In our previous correspondence you answered the following: </div><div><br></div><div>“<i>You mean this error message again?</i><div dir="ltr"><div><i><br></i></div><div><i><b style="background-color:rgb(255,255,255)"><font color="#ff0000">"eeg_checkset error: number of elements in ‘icachansind’ (55) does not match the number of columns in the sphere array (54). Should EEGlab remove ICA information (press cancel to fix the problem from the command line)”</font>. </b><br></i></div><div><b style="background-color:rgb(255,255,255)"><i><br></i></b></div><div><i>That's pretty strange...</i></div><i>One think you can try quickly is that when you use infomax, use 'pca', 58; If your current number of channels is 60, you try 59, 58, 57... I'm testing here the possibility of dimension reduction happened to your data in an unexpected reason.</i><div><i><br></i></div><div><i>EEG.icasphere has the dimension of the data decomponsed and the number of channels used, where nbchan >= data rank. When this is equal, it is called 'full rank' which is the basic assumption. Runica() has its own rank detection stage to estimate the right rank of the data, which sometimes fails.</i></div><div><i><br></i></div><div><i>I still suspect that some type of user operation caused the channel inconsistency. Are you sure you did not do any channel manipulation after ICA?<br></i><div><div><i><br></i></div><div><i>Makoto</i>” </div></div></div><div><br></div><div>I typed in what you suggested:</div><div><br></div><div><blockquote type="cite"><div dir="ltr"><div>Sorry for the trouble.</div><div>I want to know</div><div><ol><li>The number of channels (EEG.nbchan)</li><li>The number of rows in EEG.icasphere <u>right after</u> ICA</li></ol></div></div></blockquote><div>1: the number of channels is: 55</div></div><div>2: the number of rows is I think: 53 (?) I get a lot of data with zeros and the last bit of data says: Colums 53 through 55. </div><div><br></div><div>I have no idea what this means and at this point I am quite desperate because I really need this participant…</div><div><br></div><div>Thank you.</div><div><br></div><div>Best,</div><div>Edwige</div><div><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Jul 4, 2018 at 12:58 AM E. Sijyeniyo <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Dear Makoto, <div><br></div><div>I performed ICA on the dataset on which I got the error message, this time I excluded the EOG channels before ICA and therefore I didn’t click on the "…channels thing". However, surprisingly, I received the same error again.</div><div><br></div><div>Now I really don’t know what might have gone wrong.</div><div><br></div><div>Any insights on this? </div><div><br></div><div>Thank you so much for your time!</div><div><br></div><div>Best,</div><div>Edwige<br><div><br><blockquote type="cite"><div>Op 3 jul. 2018, om 19:43 heeft Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> het volgende geschreven:</div><br class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929m_4240354224116026474Apple-interchange-newline"><div><div dir="ltr">Dear Edwige,<div><br></div><div>My guess is that that's a bug in EEGLAB and caused by using that 'channels' thing.</div><div><br></div><div><span style="font-family:Arial;font-size:11pt;text-align:justify;white-space:pre-wrap;background-color:rgb(255,255,255);font-variant-east-asian:normal;vertical-align:baseline">> Click on the button </span><span style="font-family:Arial;font-size:11pt;text-align:justify;white-space:pre-wrap;background-color:rgb(255,255,255);font-style:italic;font-variant-east-asian:normal;vertical-align:baseline">... <font color="#0000ff">channels</font></span><span style="font-family:Arial;font-size:11pt;text-align:justify;white-space:pre-wrap;background-color:rgb(255,255,255);font-variant-east-asian:normal;vertical-align:baseline"><font color="#0000ff"> to select all the channels except EOGh and EOGvl</font>. The eye electrodes need to be excluded, because they don’t have the same reference as the other electrodes in our dataset. The eye electrodes are bipolar, meaning that they are referenced to each other. The other electrodes, however, are referenced to the average of all electrodes.</span><br></div><div><br></div><div>This kind of thing is poorly supported. I'm pretty sure that if you don't do it, it'll run fine. Try it.</div><div><br></div><div>If you don't include channels to ICA, what's the point of having channels... that's our way of thinking. So, if you can't include the EOG channels, reject them before ICA. Eye blinks and saccades are the things ICA can detect most dramatically, so withouot EOG channels it'll be done fine--I have absolutely no worry there.</div><div><br></div><div>By the way I like your name contains 'ewig'. Nice name.</div><div><br></div><div><i>Weh spricht 'Vergeh!'</i></div><div><i>Doch alle Lust will Ewigkeit,</i></div><div><i>will tiefe tiefe Ewigkeit!</i></div><div><br></div><div>Makoto</div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jul 3, 2018 at 5:04 AM E. Sijyeniyo <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Dear Makoto, <div><br></div><div>I tried running ICA for a dataset. Since now: I have been doing this in this order: </div><div><span id="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929m_4240354224116026474m_-8560363222264660116docs-internal-guid-eee84947-6000-f911-95e7-4b943472f53f"><ul style="margin-top:0pt;margin-bottom:0pt"><li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap;margin-left:36pt"><div style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Go to </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Tools > Run ICA</span></div></li><li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap;margin-left:36pt"><div style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Set </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">ICA algorithm to use</span><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline"> to </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">runica</span></div></li><li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap;margin-left:36pt"><div style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Click on the button </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">... channels</span><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline"> to select all the channels except EOGh and EOGvl. The eye electrodes need to be excluded, because they don’t have the same reference as the other electrodes in our dataset. The eye electrodes are bipolar, meaning that they are referenced to each other. The other electrodes, however, are referenced to the average of all electrodes.</span></div></li><li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap;margin-left:36pt"><div style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Set the </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Commandline options</span><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline"> to </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">‘extended’, 1, ‘pca’, [number of channels -3] </span><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">(Two of these three channels are the eye electrodes that you excluded. The third channel needs to be subtracted because we used average reference, which changes the rank of the data.)</span></div></li><li dir="ltr" style="list-style-type:disc;font-size:11pt;font-family:Arial;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap;margin-left:36pt"><div style="line-height:1.38;margin-top:0pt;margin-bottom:0pt;text-align:justify"><span style="font-size:11pt;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Click </span><span style="font-size:11pt;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline">Ok</span></div></li></ul></span><div>Based on your tutorial, I do not include the eye electrodes in since they were not included in the average reference: see </div><ul style="line-height:1.5em;margin:0.3em 0px 0px 1.6em;padding:0px;font-family:sans-serif;font-size:12.8px"><li style="margin-bottom:0.1em">Include EOG, ECG, and other channels as long as they share the initial reference electrode with scalp electrodes. If EOG channels are referenced to each other (i.e., bipolar), <b>exclude them.</b></li></ul><div><br></div><div>This procedure went well and I have been able to get ICs for 6 participants. However, I have done the exact procedure but now I get the warning: </div><div><b>"eeg_checkset error: number of elements in ‘icachansind’ (55) does not match the number of columns in the sphere array (54). Should EEGlab remove ICA information (press cancel to fix the problem from the command line)”. </b></div><div><b><br></b></div><div>What does this error mean? I have looked online, but I can't seem to find what I have done wrong especially because all other datasets went well with the same procedure….</div><div><br></div><div>I can definitely use your expertise on this issue. </div><div><br></div><div>Thank you so much in advance. </div><div><br></div><div>Best, </div><div>Edwige</div><div><br><blockquote type="cite"><div>Op 27 jun. 2018, om 09:53 heeft E. Sijyeniyo <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> het volgende geschreven:</div><br class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929m_4240354224116026474m_-8560363222264660116Apple-interchange-newline"><div><div style="word-wrap:break-word">Dear Makoto, <div><br></div><div>Thank you very much for your response! Ok, now I know for sure that I don’t have to reject these channels!</div><div><br></div><div><br></div><div>Best,</div><div>Edwige</div><div><div><br><blockquote type="cite"><div>Op 26 jun. 2018, om 20:02 heeft Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> het volgende geschreven:</div><br class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929m_4240354224116026474m_-8560363222264660116Apple-interchange-newline"><div><div dir="ltr">Dear Edwige,<div><br></div><div>I don't recommend to reject alpha. Alpha is a great brain component and explains most part of early visual potentials, for example. If you run ICA, it will nicely decompose it.</div><div><br></div><div>> a second year research master student<br></div><div><br></div><div>Very good! Good luck.</div><div><br></div><div>Makoto</div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jun 26, 2018 at 10:06 AM E. Sijyeniyo <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Makoto, <br><br>I am Edwige Sijyeniyo, a second year research master student in Language and Cognition at the University of Groningen (the Netherlands). <br><br>Currently, I am preprocessing my EEG data that I collected for my thesis project (name of project: Syntactic Priming in Comprehension). <br><br>I am following some of your steps at: <a href="https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_pipeline#To_learn_how_to_evaluate_EEG_and_artifact_ICs_.2801.2F24.2F2017_updated.29" rel="noreferrer" target="_blank">https://sccn.ucsd.edu/wiki/Makoto%27s_preprocessing_pipeline#To_learn_how_to_evaluate_EEG_and_artifact_ICs_.2801.2F24.2F2017_updated.29</a> <br><br>I had a question regarding interpolation of bad channels, some participants show a lot of alpha waves (especially in the posterior electrodes like PO9, PO10, PO7, PO8 etc). I was wondering whether channels that contain a lot of alpha waves can be interpolated, therefore marking these channels as noisy <br><br>Would alpha waves distort the data to a large extent if these are not interpolated? <br><br>Thank you so much for your time and am looking forward to your response!<br><br>Best,<br>Edwige <br><br><br></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929m_4240354224116026474m_-8560363222264660116gmail_signature"><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div></div></div></div></blockquote></div><br></div></div></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929m_4240354224116026474gmail_signature"><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div></div></div></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div><div><br><blockquote type="cite"><div>Op 6 jul. 2018, om 21:03 heeft Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> het volgende geschreven:</div><br class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929Apple-interchange-newline"><div><div dir="ltr">Dear Edwige,<div><br></div><div>Sorry for the trouble.</div><div>I want to know</div><div><ol><li>The number of channels (EEG.nbchan)</li><li>The number of rows in EEG.icasphere <u>right after</u> ICA</li></ol><div>They should match. If they don't, it must be EEGLAB bug--in that case, we may need to ask you to send us the dataset. Let us know what you get.</div></div><div><br></div><div>Makoto</div><br><div class="gmail_quote"><div dir="ltr">On Fri, Jul 6, 2018 at 10:32 AM E. Sijyeniyo <<a href="mailto:e.sijyeniyo@student.rug.nl" target="_blank">e.sijyeniyo@student.rug.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Dear all, <div><br></div><div>While running ICA for one of my participants, I received the following error message: </div><div><br></div><div><b>"eeg_checkset error: number of elements in ‘icachansind’ (55) does not match the number of columns in the sphere array (54). Should EEGlab remove ICA information (press cancel to fix the problem from the command line)”. </b></div><div><b><br></b></div><div>I have done the preprocessing procedure for this participant the same way in which I have done others. However, for my other participants, I did not get this message, only for this one participant. </div><div><br></div><div>What I typed in the <i>Commandline</i> after selecting for runica is -> <span style="text-align:justify;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap"> </span><span style="text-align:justify;font-style:italic;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">‘extended’, 1, ‘pca’, [number of channels -1] </span><span style="text-align:justify;font-variant-ligatures:normal;font-variant-east-asian:normal;vertical-align:baseline;white-space:pre-wrap">(-1 is because I used average reference which changes the rank of the data).</span></div><div><br></div><div>Does anyone know what this error mean? I tried running ICA for the same participant again, but I keep getting the same error…could this be a bug? </div><div><br></div><div>Thank you so much in advance!</div><div><br></div><div>Best, </div><div>Edwige<br><div><br></div><div><br></div></div></div>_______________________________________________<br>
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</div></blockquote><div><div><div dir="ltr"><div dir="ltr" class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail-m_-1392795611737945929gmail_signature"><div dir="ltr"><br></div></div></div></div></div></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_-3323439657313735903m_4635028319333169514m_1413870519219806402gmail_signature"><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div></div></div></div></div>
</blockquote></div><br></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="m_-3323439657313735903gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Makoto Miyakoshi<br>Swartz Center for Computational Neuroscience<br>Institute for Neural Computation, University of California San Diego<br></div></div></div>