<div dir="ltr"><span style="font-family:Calibri,sans-serif;line-height:16.363636016845703px"><font size="3">> I was curious about </font></span><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">whether it is possible to include different frequency ranges (delta, alpha...) in component clustering seperately.</span><br>
<div class="gmail_extra"><br></div><div class="gmail_extra">You can specify the freq range in ERSP when preclustering. However, if you want to include multiple ranges, that's impossible. Also, if you want to test the difference across freq ranges, you need to repeat preclustering separately for each range, and the results should be treated as separate too. You can't do multiple frequency range clustering with different weights etc.</div>
<div class="gmail_extra"><br></div><div class="gmail_extra"><font face="Calibri, sans-serif" size="3"><span style="line-height:16.363636016845703px">> I am confused since the spectra (plot spectra) remains the same independently of the 'frequrange'(?) I add. </span></font><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">However, on the matlab file (Study-cluster, specdata) the frequency-bins change correspondingly. </span><br>
</div><div class="gmail_extra"><br></div><div class="gmail_extra">I don't understand this. Is this a spectrum curve or ERSP? Please tell us more details.</div><div class="gmail_extra"><br></div><div class="gmail_extra">
<span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">> By the way, what information does the file "specfreqs" contain? </span><br></div><div class="gmail_extra"><br>
</div><div class="gmail_extra">I don't to know off the top of my head...Which function takes this option, do you know? </div><div class="gmail_extra"><br></div><div class="gmail_extra">Makoto</div><div class="gmail_extra">
<br><div class="gmail_quote">2014-05-14 14:02 GMT-07:00 <span dir="ltr"><<a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</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">
<font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif"><font face="Verdana, Arial, Helvetica, sans-serif">Dear Makoto</font><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><br></div><div><font face="Verdana, Arial, Helvetica, sans-serif">Thanks for the insightful inputs. </font></div>
<div><font face="Verdana, Arial, Helvetica, sans-serif"><br></font></div><div><font face="Verdana, Arial, Helvetica, sans-serif">I guess 'timerange' [min max] is the </font><span style="font-family:Calibri,sans-serif;line-height:16.363636016845703px"><font size="3">spectopo parameter for including a power baseline. </font></span></div>
<div><span style="font-family:Calibri,sans-serif;line-height:16.363636016845703px"><font size="3"><br></font></span></div><div><span style="font-family:Calibri,sans-serif;line-height:16.363636016845703px"><font size="3">Thanks for referring to the code for exporting grouped frequency values. However, I was curious about </font></span><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">whether it is possible to include different frequency ranges (delta, alpha...) in component clustering seperately. This might be </span><font face="Calibri, sans-serif" size="3"><span style="line-height:16.363636016845703px">advantageous since less tests (per Hz) have to be done, decrasing the number of multiple corrections. I am confused since the spectra (plot spectra) remains the same independently of the 'frequrange'(?) I add. </span></font><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">However, on the matlab file (Study-cluster, specdata) the frequency-bins change correspondingly. </span></div>
<div><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px"><br></span></div><div><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">By the way, what information does the file "specfreqs" contain? </span></div>
<div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif">
<span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px">Lars</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px"><br>
</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif">
<span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:medium;line-height:16.363636016845703px"><br>
</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><div class=""><br><font color="#990099">-----Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> schrieb: -----</font></div>
<div style="padding-left:5px"><div style="padding-right:0px;padding-left:5px;border-left-style:solid;border-left-color:black;border-left-width:2px"><div class="">An: <a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</a><br>
Von: Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br></div>Datum: 12.05.2014 17:52<br>Kopie: EEGLAB List <<a href="mailto:eeglablist@sccn.ucsd.edu" target="_blank">eeglablist@sccn.ucsd.edu</a>><div>
<div class="h5"><br>Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using the Automatic Artifact Removal (AAR) toolbox<br><br><div dir="ltr"><font face="arial, helvetica, sans-serif">Dear Lars,</font><div>
<font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><span style="line-height:16.866666793823242px">> For example, how do I run a spectro-analysis with a </span><span style="line-height:16.866666793823242px">90% overlapping Hanning window of 1 s (</span><span style="line-height:16.866666793823242px">512-point short-time Fourier transform) including a baseline (</span><span style="line-height:16.866666793823242px">mean baseline power) </span><span style="line-height:16.866666793823242px">within the stimulus, and with log-converted power values (dB)?</span><br>
</font></div><div><span style="line-height:16.866666793823242px"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><font face="arial, helvetica, sans-serif"><span style="line-height:16.866666793823242px">Go to </span><span style="line-height:16.866666793823242px"><a href="http://sccn.ucsd.edu/pipermail/eeglablist/2014/thread.html" target="_blank">http://sccn.ucsd.edu/pipermail/eeglablist/2014/thread.html</a> and find this thread</span></font></div>
<div><font face="arial, helvetica, sans-serif">[Eeglablist] How to change FFT parameters?<span style="line-height:16.866666793823242px"><br>
</span></font></div><div><font face="arial, helvetica, sans-serif">See what Arno says there.</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><span style="line-height:16.866666793823242px">> How would I caluclate relative (vs. absolute) dB?</span><br>
</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">In EEGLAB, 1uV peak-to-peak sine wave power is defined to be 0dB;, 10uV is 20dB, 0.1uV is -20dB etc.</font></div>
<div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><span style="line-height:16.866666793823242px">> Is it possible to run the spectro-analysis in grouped frequency ranges (e.g., delta, theta, alpha, beta, gamma) seperately? What would be the code I would have to add in the interface? I am a bit confused, since the Freq.range [Hz] on the "Build preclustering array"interface is by default "3 25" and by changing it would not change the output.</span><br>
</font></div><div class="gmail_extra"><div><span style="line-height:16.866666793823242px"><font face="arial, helvetica, sans-serif"><br></font></span></div><div>
<div><font face="arial, helvetica, sans-serif"><span style="line-height:16.866666793823242px">Go to </span><span style="line-height:16.866666793823242px"><a href="http://sccn.ucsd.edu/pipermail/eeglablist/2014/thread.html" target="_blank">http://sccn.ucsd.edu/pipermail/eeglablist/2014/thread.html</a> and find this thread</span></font></div>
<div><font face="arial, helvetica, sans-serif">[Eeglablist] Extracting data in frequency ranges from dataset<br></font></div></div><div>
<span style="line-height:16.866666793823242px"><font face="arial, helvetica, sans-serif">Find my replies. You can find code for that.</font></span></div><div><span style="line-height:16.866666793823242px"><font face="arial, helvetica, sans-serif"><br>
</font></span></div><div><span style="line-height:16.363636016845703px"><font face="arial, helvetica, sans-serif">> And two questions concerning statistics: Does the sampling rate have an impact on (permutation) statistics? Currently, I am using a sampling rate of 500. I would probably have to down-sample if it increases multiple corrections. </font></span></div>
<div><span style="line-height:16.363636016845703px"><font face="arial, helvetica, sans-serif"><br></font></span></div><div>
<span style="line-height:16.363636016845703px"><font face="arial, helvetica, sans-serif">Although I don't have mathematical proof, I would say no.</font></span></div><div>
<span style="line-height:16.363636016845703px"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="line-height:16.363636016845703px"><font face="arial, helvetica, sans-serif">> And finally, I can't find a file with the statistical values. I assume I would just have to click on the cluster I am interested and select the statistics ("STATS") and plot spectra. Then matlab should create a new file, right?</font></span></div>
</div><div class="gmail_extra"><font face="arial, helvetica, sans-serif"><br></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif">If you want to extract statistics results, you need to run it from command line. I strongly believe that this should be fixed so that users can access result values. Let me show you a temporally solution for a workaround. In STUDY edit/plot GUI, show spectra for all clusters. Press 'ok' and close the edit/plot GUI to make EEGLAB updated. In the Matlab workspace, click 'STUDY-cluster(1,x) where x is your desired cluster - spectra (or something like that). You can find stacked arrays of spectra in the order of conditions (conditions are separated as cell), frequency, and ICs. You can run statistics on your own using these values.</font></div>
<div class="gmail_extra"><font face="arial, helvetica, sans-serif"><br></font></div><div class="gmail_extra"><font face="arial, helvetica, sans-serif">Makoto</font></div><div class="gmail_extra"><br></div><div class="gmail_extra">
<div class="gmail_quote">2014-05-12 4:20 GMT-07:00 <span dir="ltr"><<a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</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"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif"><font face="Verdana, Arial, Helvetica, sans-serif">Dear Makoto</font><div style="font-family:Verdana,Arial,Helvetica,sans-serif">
<br></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif">Thank you very much for your help on the time-frequency analysis. <span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">However, since EEGlab has been </span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">updated recently, the problem ("Inner matrix dimensions
must agree") did not occur anymore. Thus, the problem is solved.</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%"><br>
</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span lang="EN-US" style="font-size:11pt;line-height:115%;font-family:Calibri,sans-serif">Currently,
I am analyzing spectra on the level of IC clusters. However, even though I
studied the manual carefully, I don t fully understand how to use these spectopo parameters provided on </span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">the interface “Precompute component measures ”(Power spectrum). I was wondering whether you could </span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">share your
knowledge on this. I would be really thankful!</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif">
<span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">For example, how do I run a spectro-analysis with a </span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">90%
overlapping Hanning window of 1 s (</span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">512-point
short-time Fourier transform) including a baseline (</span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">mean
baseline power) </span><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">within the stimulus, and with log-converted power values (dB)?</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif">
<span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">How would I caluclate relative (vs. absolute) dB?</span></div>
<div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%">Is it possible to run the spectro-analysis in grouped frequency ranges (e.g., delta, theta, alpha, beta, gamma) seperately? What would be the code I would have to add in the interface? I am a bit confused, since the Freq.range [Hz] on the "Build preclustering array"interface is by default "3 25" and by changing it would not change the output.</span></div>
<div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:Calibri,sans-serif;font-size:11pt;line-height:115%"><br></span></div><div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px">And two questions concerning statistics: Does the sampling rate have an impact on (permutation) statistics? Currently, I am using a sampling rate of 500. I would probably have to down-sample if it increases multiple corrections. And finally, I can't find a file with the statistical values. I assume I would just have to click on the cluster I am interested and select the statistics ("STATS") and plot spectra. Then matlab should create a new file, right?</span></font></div>
<div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px"><br></span></font></div><div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px">I hope these arent too many questions. Thousand thanks!!!</span></font></div>
<div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px"><br></span></font></div><div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px">best, Lars</span></font></div>
<div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px"><br></span></font></div><div><font face="Calibri, sans-serif"><span style="font-size:14.545454025268555px;line-height:16.363636016845703px"><br>
</span></font></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif"><br></span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif"><br>
</span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif"> </span></div><div style="font-family:Verdana,Arial,Helvetica,sans-serif"><div><br><font color="#990099">-----Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> schrieb: -----</font></div>
<div style="padding-left:5px"><div style="padding-right:0px;padding-left:5px;border-left-style:solid;border-left-color:black;border-left-width:2px"><div>An: <a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</a><br>
Von: Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br></div>Datum: 15.04.2014 17:34<div><div><br>Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using the Automatic Artifact Removal (AAR) toolbox<br>
<br><div dir="ltr">Dear Lars,<div><br></div><div>Sorry for delay.</div><div>I found you sent me the document that says your size(EEG.icaact,1) == 0, which is a problem. This means that you don't have independent component activation.</div>
<div><br></div><div>Do you have ICA matrix? Check your main EEGLAB GUI to see whether ICA is yes. If it's yes AND size(EEG.icaact,1) == 0, that is pathological. You should try this code</div><div><br></div><div>EEG = eeg_checkset(EEG, 'ica');</div>
<div><br></div><div>although I don't understand why you don't have EEG.icaact... and if you don't have EEG.icaact you should not have been able to compute component cross coherence.</div><div><br></div><div>Could you check you EEG.data also? Does it say 'mmo' (memory mapping object) by any chance? If that's the case, then you should do</div>
<div><br></div><div>EEG.data = EEG.data(:,:,:);</div><div><br></div><div>to retrieve all data into RAM. I hate this memory mapping object since this is not compatible with many EEGLAB functionis and causes troubles everywhere. This memory mapping option comes with (I believe) Mobilab. In the EEGLAB set up option you may find an item for this memory mapping object. TURN IT OFF if it is ever checked 'on'!</div>
<div><br></div><div>Makoto</div><div><br></div><div>Makoto</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-04-07 3:01 GMT-07:00 <span dir="ltr"><<a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</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"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif">Dear Makoto<br>
<br>I
pasted the following code and received a large message. I copied it in a
word file and attached it. I further attached my dataset for
toubleshooting.<br>I am still struggling with this error. I really appreciate your help.<br><br>Best regards,<br>Lars</font><div><br><br><font color="#990099">-----Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>> schrieb: -----</font></div>
<div style="padding-left:5px"><div style="padding-right:0px;padding-left:5px;border-left-style:solid;border-left-color:black;border-left-width:2px"><div>An: <a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</a><br>
Von: Makoto Miyakoshi <<a href="mailto:mmiyakoshi@ucsd.edu" target="_blank">mmiyakoshi@ucsd.edu</a>><br></div>Datum: 05.04.2014 04:26<div><br>Betreff: Re: [Eeglablist] Repairing non-stereotyped artifacts using using the Automatic Artifact Removal (AAR) toolbox<br>
<br></div><div dir="ltr"><div>Dear Lars,</div><div><br></div><div>Check the following, copy and paste what you find. I may be able to find something there.<div><br></div><div>EEG.icachansind</div><div>size(EEG.icaact,1)</div>
<div>EEG.nbchan</div>
<div>EEG.history</div><div><br></div><div>If this does not work... you may need to send me a sample data for troubleshooting. It's highly likely that this is not an EEGLAB bug, but I'd be happy to help you anyways!</div>
<div><br></div><div>Makoto</div><div><br></div></div></div><div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-04-03 5:05 GMT-07:00 <span dir="ltr"><<a href="mailto:lars.rogenmoser@psychologie.uzh.ch" target="_blank">lars.rogenmoser@psychologie.uzh.ch</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"><font face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif">As I mentioned, on channel level I am able to plot time-frequency and also cross-coherence. In fact, I am also able to run component cross-coherence, but unfortunately no component time-frequency which seems to be quite strange. I receive the error <span style="font-family:'Sans Serif',Verdana,Arial,Helvetica,sans-serif">"Inner matrix dimensions must agree".<br>
<br>I imported vhdr-files recorded from Geodesics-system. I used a self-generated channel location (please find attached), however I read this template over "read locations" and chose the "BESA or EGI-3D cartesian .sfp file" format, ending up with 109 channels. My sampling rate is 500 Hz. I tried lowering the sampling rate (250 Hz) but the problem remained. I re-referenced using an averaged reference. I filtered 1-100 Hz (Basic FIR filter) and used the cleanline algorithm. I removed segemnts on which the subjects responded (select data using events), ending up with a dataset with segemnts of interest. I ran ASR and then ICA (extended), of course excluding noisy channels before. I then epoched the segemnts (extract epoches) beloning to the same conditions. Precisely, I have 4 segements per conditions however with a lenght of 1 minute (+5 sec pre-stimulus). I haven t removed the baseline or corrected anything in this circumstance. <br>
<br>Furthermore, I re-named the types of the triggers (Event values) and also co-registered channel location with head mesh (colin27headmesh). I am using the latest version of EEGlab and Matlab R2013b.<br><br>I really hope this helps.<br>
<br>Best, Lars<br><br><br><br><br></span><div><br><br><br></div></font></blockquote></div></div>
</div></div></div><div></div></font></blockquote></div><br><br clear="all"><div><br></div>-- <br><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></div></div><div></div></font></blockquote></div><br><br clear="all"><div><br></div>-- <br><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></div></div></div><div></div></font></blockquote></div><br><br clear="all"><div><br></div>-- <br><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>