<div dir="ltr">Dear Martin,<div><br></div><div>> after which I save cleanEEG as a set (containing all conditions) and use this in the STUDY.<br><div class="gmail_extra"><br></div><div class="gmail_extra">Yes, but if your experimental design is event-related potential analysis, you need to epoch your data first.</div><div class="gmail_extra"><br></div><div class="gmail_extra">Makoto</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 20, 2016 at 11:24 AM, Martin Randau <span dir="ltr"><<a href="mailto:cmmrandau@gmail.com" target="_blank">cmmrandau@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div><div>Hello again Clement and Makoto<br><br></div>I forgot to cc Makoto in my reply to Clement. My question is whether doing the following is the correct way when I want to run two ICA on the same dataset first on contionous data and again after removing bad epochs:<br><br></div><blockquote>contEEG = pop_runica(EEG);<br><br></blockquote></div><blockquote>% removing epochs<br><br></blockquote></div><blockquote>cleanEEG = pop_runica(contEEG);</blockquote><br><br></div>after which I save cleanEEG as a set (containing all conditions) and use this in the STUDY.<br><br></div>Best wishes,<br></div>Martin<br></div><div class="gmail_extra"><span class="gmail-"><br clear="all"><div><div class="gmail-m_-5332465824529364626gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><div>Venlig hilsen / Best wishes<br>Martin<br></div><br></div><div>Stud. Med. <br></div><div>University of Copenhagen<br></div><div><br></div>Center for Neuropsychiatric Schizophrenia Research (CNSR) &
Center for Clinical Intervention and Neuropsychiatric Schizophrenia
Research (CINS)
<div>Copenhagen University Hospital<br>Psychiatric Centre Glostrup<br>Ndr. Ringvej <br>DK-2600 Glostrup<br>Denmark</div>
e-mail: <a href="mailto:nikolaj@cnsr.dk" target="_blank">cmmrandau@gmail.com</a> <br>phone: <a href="tel:%2B45%203864%200844" value="+4538640844" target="_blank">+45 42744285</a></div><div><div><div><br><div><div><div><div><br></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div class="gmail_quote">2016-10-20 18:33 GMT+02:00 Clement Lee <span dir="ltr"><<a href="mailto:cll008@eng.ucsd.edu" target="_blank">cll008@eng.ucsd.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Oh yes I misread your question. I'm not too familiar with running ICA twice, but doing it the way I wrote would NOT use the old ICA weights.</div><div class="gmail-m_-5332465824529364626HOEnZb"><div class="gmail-m_-5332465824529364626h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 20, 2016 at 8:39 AM, Martin Randau <span dir="ltr"><<a href="mailto:cmmrandau@gmail.com" target="_blank">cmmrandau@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><p dir="ltr">Thank you Clement, I will try this. But don't you mean </p>
<p dir="ltr">cleanEEG = pop_runica(contEEG) so that we apply the second ICA to contEEG that came out of the first ICA? </p>
<p dir="ltr">Best wishes,<br>
Martin </p><div><div class="gmail-h5">
<div class="gmail_extra"><br><div class="gmail_quote">On Oct 18, 2016 21:47, "Clement Lee" <<a href="mailto:cll008@eng.ucsd.edu" target="_blank">cll008@eng.ucsd.edu</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">No problem at all. Keep us posted and let us know if you run into any problems.<div><br></div><div>For scripting ICA twice, what you have should work as long as you save after the first instance and before the second. Alternatively, it may be better practice to use something like 'contEEG' and 'cleanEEG' as variable names to keep a clear record.</div><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><div><br></div><div>contEEG = pop_runica(EEG); % ica of continuous EEG</div><div><br></div><div>%% remove bad epochs of EEG; </div></blockquote><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><div>% steps to clean bad epochs here in this section</div><div>%%</div><div><br></div></blockquote><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><div>cleanEEG = pop_runica(EEG) % ica of cleaned EEG</div></blockquote><br><div>Of course, for any processes thereafter you would call 'contEEG' or 'cleanEEG' instead of just 'EEG'.</div><div><br></div><div>Clement</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 18, 2016 at 12:32 PM, Martin Randau <span dir="ltr"><<a href="mailto:cmmrandau@gmail.com" target="_blank">cmmrandau@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div>Dear Clement and Makoto,<br><br></div>Thank you for your replies. I think the problem was that I had created separate sets for each condition. I am currently re-processing my test data consisting of 30 subjects (15 patients and 15 controls) and expect this to be ready by Thursday (my computer is not the fastest available).<br><br></div>My setup is EEG data on an oddball paradigm (standard stimulus, duration deviant, frequency deviant and frequency+duration deviant) in order to analyze MMN, much like the Rissling, Makeig et al article. We have data from about 100 subjects in total.<br><br>I run a pre-processing pipeline much inspired by Makoto's pipeline but I run 2x ICA, one on continous data and one after removal of 5-10% bad epochs. I then create 4 separate sets for each stimulus type and load them into a STUDY as different conditions. This last part seems to be the problem! <br><br>In my new setup I have one set per subject and divide the two groups (patient and control) as different 'conditions' instead of 'groups', and plan to use 'events' as markers for the stimulus types. <br><br></div>I also had some problems using std_selectICsByCluster but I suspect this is also because I had different sets for the conditions.<br><br></div>I will get back to you on Thursday or Friday when I have tested my new data.<br><br></div>While I have you on the line, I have another question regarding running ICA twice. In my script I simply have EEG = pop_runica(EEG) twice, once before epoching and again after removing bad epochs. Is this the correct way, or am I running a new ICA and not including the old weights? I have read on the list about applying ICA weights to the data but I have not studied this further, as I assumed running pop_runica a second time automatically includes the old ICA. <br><br></div>Once again, thank you for taking the time to help out! :)<br></div><div class="gmail_extra"><span><br clear="all"><div><div class="gmail-m_-5332465824529364626m_829419659770227261m_2725323328770160735m_-3538197375798658433m_-8986139902175364335gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><div>Venlig hilsen / Best wishes<br>Martin<br></div><br></div><div>Stud. Med. <br></div><div>University of Copenhagen<br></div><div><br></div>Center for Neuropsychiatric Schizophrenia Research (CNSR) &
Center for Clinical Intervention and Neuropsychiatric Schizophrenia
Research (CINS)
<div>Copenhagen University Hospital<br>Psychiatric Centre Glostrup<br>Ndr. Ringvej <br>DK-2600 Glostrup<br>Denmark</div>
e-mail: <a href="mailto:nikolaj@cnsr.dk" target="_blank">cmmrandau@gmail.com</a> <br>phone: <a href="tel:%2B45%203864%200844" value="+4538640844" target="_blank">+45 42744285</a></div><div><div><div><br><div><div><div><div><br></div></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div class="gmail-m_-5332465824529364626m_829419659770227261m_2725323328770160735m_-3538197375798658433h5"><div class="gmail_quote">2016-10-18 21:06 GMT+02:00 Clement Lee <span dir="ltr"><<a href="mailto:cll008@eng.ucsd.edu" target="_blank">cll008@eng.ucsd.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Sorry for your troubles Martin, and thanks for reporting the issue. In addition to Makoto's questions, I'm curious if you used any optional inputs while running std_envtopo, and whether or not you used an older version of std_envtopo on the same dataset before downloading the current version.<span class="gmail-m_-5332465824529364626m_829419659770227261m_2725323328770160735m_-3538197375798658433m_-8986139902175364335HOEnZb"><font color="#888888"><div><br></div><div>Clement</div></font></span><div><div class="gmail-m_-5332465824529364626m_829419659770227261m_2725323328770160735m_-3538197375798658433m_-8986139902175364335h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 18, 2016 at 12:51 AM, 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Dear Martin,<div><br></div><div>Sorry for inconvenience.</div><div><br></div><div><font color="#ff0000">Error using *<br>Inner matrix dimensions must agree.<br><br>Error in std_envtopo (line 322)<br> convTopoErp{1, cls}{columnwise,rowwise} = tmpTopo3*erp; </font><br></div><div class="gmail_extra"><br></div><div class="gmail_extra">Hmm this means you have different number of IC topos and ERPs. How could it be possible? I definitely need more info to troubleshoot this. What's your STUDY design, and how did you create STUDY? Did you, for example, separate conditions into different .set files?</div><div class="gmail_extra"><br></div><div class="gmail_extra">Makoto</div><div class="gmail_extra"><br></div><div class="gmail_extra"><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 10, 2016 at 1:22 AM, Martin Randau <span dir="ltr"><<a href="mailto:cmmrandau@gmail.com" target="_blank">cmmrandau@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hello all,<br><div><br>I am having problems with the plugin std_envtopo. When running it from the gui on a study composed of 2 groups with 4 conditions each fresh after clustering I get this error:<br><br><blockquote>Error using *<br>Inner matrix dimensions must agree.<br><br>Error in std_envtopo (line 322)<br> convTopoErp{1, cls}{columnwise,rowwise} = tmpTopo3*erp; %min abs =<br> zero<br><br>Error in gui_std_envtopo>startButton_Ca<wbr>llback (line 560)<br>STUDY = std_envtopo(STUDY, ALLEEG, arguments{:});<br><br>Error in gui_mainfcn (line 96)<br> feval(varargin{:});<br><br>Error in gui_std_envtopo (line 42)<br> gui_mainfcn(gui_State, varargin{:});<br><br>Error in<br>@(hObject,eventdata)gui_std_en<wbr>vtopo('startButton_Callback',h<wbr>Object,eventdata,guidata(hObje<wbr>ct))<br><br> <br>Error while evaluating uicontrol Callback</blockquote><div><div>Sometimes the error goes away after running the 'precompute component measures' -> 'build preclustering array' -> 'cluster components' but this is often not the case. I do not know what is causing the error, so please let me know if you need more information. I am able to plot everything (scalp maps, ERP, dipoles, power spectrum) from the 'edit/plot clusters' menu. Number of sessions, conditions and groups are consistent in the dataset.<br><br><br clear="all"><div><div class="gmail-m_-5332465824529364626m_829419659770227261m_2725323328770160735m_-3538197375798658433m_-8986139902175364335m_-2416736054733668775m_-5599449754252668647gmail-m_-6972430818643483882gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><div>Venlig hilsen / Best wishes<br>Martin<br></div><br></div><div>Stud. Med. <br></div><div>University of Copenhagen<br></div><div><br></div>Center for Neuropsychiatric Schizophrenia Research (CNSR) &
Center for Clinical Intervention and Neuropsychiatric Schizophrenia
Research (CINS)
<div>Copenhagen University Hospital<br>Psychiatric Centre Glostrup<br>Ndr. Ringvej <br>DK-2600 Glostrup<br>Denmark</div>
e-mail: <a href="mailto:nikolaj@cnsr.dk" target="_blank">cmmrandau@gmail.com</a> <br>phone: <a value="+4538640844" href="tel:%2B45%203864%200844" target="_blank">+45 42744285</a></div><div><div><div><br><div><div><div><div><br></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="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>
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