<div dir="ltr">Hi Virginie,<div><br></div><div>glad you are finally using our ICA ;)</div><div class="gmail_extra">Let me reply inline:</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Oct 13, 2015 at 11:09 AM, Virginie van Wassenhove <span dir="ltr"><<a href="mailto:virginie.van.wassenhove@gmail.com" target="_blank">virginie.van.wassenhove@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"><div>Hi </div><div><br></div><div>some comments on inconsistencies found on <a href="http://martinos.org/mne/dev/auto_tutorials/plot_ica_from_raw.html" target="_blank">http://martinos.org/mne/dev/auto_tutorials/plot_ica_from_raw.html</a> also observed when actually performing ICA on data.</div><div><br></div><div>In your tutorial, you use: n_max_ecg, n_max_eog = 3,1</div><div><br></div><div>Then you effectively find 3 components for ECG (in red in the graphs: IC 59, 33 and 32) but 2 components for EOG (IC 39 and 59)in section 2.</div><div>1. If we understand properly, IC 59 captures both ECG and EOG arfifacts, is this correct? <br></div><div>2. In section 3, there are four components showing up in read on the top left graph and these are IC 33, 34, 40, and 60. There's a problem of numbering here? Shift of 1???</div><div><br></div></div></blockquote><div><br></div><div>You pick n_max_XXX components effectively, but the algorithm may propose more above threshold components. You pick the k first biggest, sorted by score.</div><div>Then the index shift is a peculiarity, as long as you are looking at component plots you see indices.</div><div>Once you look at ICA components in a Raw or Epochs object (ica.get_sources or certain plot methods) the numbers refer to channel names and hence regular numbers. I know it can be confusing, we will eventually find a solution.</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div>In our data: </div><div>we applied ICA to raw data : <br></div><div>- we used the same codes specifying n_max_ecg, n_max_eog = 3,3</div><div>- 2 components were found for ECG (IC 0 and IC 38 in red with the indexing starting at 0) </div><div><br></div><div><img src="cid:ii_150606bf80b498ed" alt="Inline image 2" width="563" height="284"><br></div><div><br></div></div></blockquote><div><br></div><div>The SNR of the detection metric looks very good.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div>- 2 components are found for EOG (4 in red; 2 for each EOG channels (vertical and horizontal, I am assuming the scores below are or each EOG channel)<br></div><div><br></div></div></blockquote><div><br></div><div>yes, two channels, you also see that the one component does not score high on the other channel.</div><div>we could improve the labeling here.</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><img src="cid:ii_150606f0c78ee48b" alt="Inline image 3" width="563" height="284"><br></div><div><br></div><div><br></div><div>When using the ica.plot_sources for ECG only, 3 components (ICA 001; 007; 039) show up in red even though the ecg_inds only contains 2 components (indices 0 and 38). Thus, 2 problems here: you need fix the indices issues (??) and why 3 components and not 2?</div><div><br></div></div></blockquote><div><br></div><div>there is no indexing issue. I fear while trying to make this consistent we stopped somewhere in the middle.</div><div> <br></div><div>the overlay plots are not selective, they just display all components that are marked bad.</div><div>Currently we do not have an API or data structure that gives you post hoc reasons for which a component was selected. Could be improved if enough people say this is important to them.</div><div>Apparently the late ECG wave looks like an EOG for this ICA solution, so you have 3 components, ok?</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><br></div><div><img src="cid:ii_15060715dc1dcb84" alt="Inline image 4" width="563" height="424"><br></div><div><br></div><div>With this, I am unsure of which ICA are actually being applied in the next steps.</div><div><br></div><div>For the EOG, the exact same 3 component names are indicated on the figure and eog_inds = [6, 38]</div><div><br></div></div></blockquote><div><br></div><div>see above</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div><img src="cid:ii_1506073bd3272c25" alt="Inline image 5" width="563" height="424"><br></div><div><br></div><div><br></div><div>Can you please explain what is correct and what is not above? and see in the codes where indices get lost etc...</div><div><br></div></div></blockquote><div><br></div><div>Let me know if it is clearer now.</div><div><br></div><div>Best,</div><div>Denis</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div></div><div>Thanks, best wishes, </div><span class="HOEnZb"><font color="#888888"><div>Virginie</div><div><br></div><div><br></div><div><br></div><div><br></div><br clear="all"><div><br></div>-- <br><div><div dir="ltr"><div><div dir="ltr"><font size="1">Virginie van Wassenhove<br><a href="mailto:Virginie.van.Wassenhove@gmail.com" target="_blank">Virginie.van.Wassenhove@gmail.com</a></font></div><div><span style="font-size:x-small">work: <a href="tel:%2B33%280%291.69.08.1667" value="+33169081667" target="_blank">+33(0)1.69.08.1667</a></span><br></div><div><span style="font-size:x-small">skype: virginie_vw</span></div><div dir="ltr"><font size="1"><a href="https://sites.google.com/site/virginievanwassenhove/" target="_blank">https://sites.google.com/site/virginievanwassenhove/</a></font><br></div></div></div></div>
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