<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">2016-10-26 12:02 GMT-05:00 Eric Larson <span dir="ltr"><<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I know it has been a while, but I finally went back to this project and managed to create the DigMontage using the mne.channels.read_dig_montage.<wbr>..<span class=""><div>It works, but I'm not sure if this is the correct way to do it.<br></div></span></div></blockquote><div><br></div><div>Given that your alignments look approximately correct (other than the scaling issue!) I suspect these steps are correct. Can you open an MNE-Python issue with this procedure? It would be good if we could turn it into a tutorial or improve the docs to describe it.</div></div></div></div></blockquote><div><br></div><div>I opened the issue in github, I can help to write the tutorial.</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 class="gmail_extra"><div class="gmail_quote"><span class=""><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><b>Is it ok to use electrodes as head points?</b></div></div></blockquote><div><br></div></span><div>If you don't have "extra" points directly on the scalp, I would say that electrodes can be used, yes. But keep in mind how your digitization was actually done during the experiment; some electrodes (e.g., <a href="http://www.brainproducts.com/productdetails.php?id=4" target="_blank">BrainVision actiCap</a>) are actually a bit thick, say half a centimeter, so if they were digitized on the center of those electrodes, you'd expect them to be that far off of the MRI during coregistration.</div></div></div></div></blockquote><div><br></div><div>Indeed, I think this is what is happening. I'm checking to see if this was the case.</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 class="gmail_extra"><div class="gmail_quote"><span class=""><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><b>Is it not enough to use the fiducials alone?</b></div></div></blockquote><div><br></div></span><div>You can use just the fiducials, but fitting a the rotation + translation using three points manually placed on an MRI surface is might be less robust than fitting extra dig points. So it depends on how much you trust your fiducial digitization and your ability to pinpoint those equivalent locations no an MRI.</div></div></div></div></blockquote><div><br></div><div>I see, the problem is the noise in the acquisition of the fiducials, which could be minimized by extra points assuming the error in measurement is gaussian. I always wandered why the extra points if three is enough in the ideal world ;)</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 class="gmail_extra"><div class="gmail_quote"><span class=""><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>Perhaps I should open a new thread less specific about eximia, since my question is more generic:<b> how can I align electrodes to individual MRIs just having the fiducials from the digitization process in a text file?</b></div></div></blockquote><div><br></div></span><div>We have an <a href="https://github.com/mne-tools/mne-python/pull/3523" target="_blank">eXimia data-reading pull request open</a>, and support is a work-in-progress. So I suggest we discuss eXimia things there to converge on something usable.</div></div></div></div></blockquote><div><br></div><div>Since I do not have Eximia EEG data in this project (.nxe), I think it is a bit different from this thread.</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 class="gmail_extra"><div class="gmail_quote"><div><br></div><div>The digitization issues are more generic, and hopefully someone else can comment more meaningfully. I don't have much experience with it. But in theory once you have your info['dig'] populated properly via DigMontage, using the coreg gui in MNE-Python, or even saving the data to FIF and using mne_analyze should be possible. But it sounds like you have already gone that route...</div></div></div></div></blockquote><div><br></div><div>yes, I'm just not sure which is the best/simpler way of doing it.</div><div>For instance I think it is weird to call set_montage twice...</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 class="gmail_extra"><div class="gmail_quote"><span class=""><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>However, for some reason all the electrodes are quite far from the scalp, even though the fiducials were aligned:<br></div><div><br></div><div><a href="https://drive.google.com/open?id=0B0p7WZ2wlTFSNklmcTlPakJERXc" target="_blank">https://drive.google.com/open?<wbr>id=0B0p7WZ2wlTFSNklmcTlPakJERX<wbr>c</a><br></div><div><a href="https://drive.google.com/open?id=0B0p7WZ2wlTFScXF4NGMtNXBiZ2M" target="_blank">https://drive.google.com/open?<wbr>id=0B0p7WZ2wlTFScXF4NGMtNXBiZ2<wbr>M</a><br></div><div><br></div><div>since it happened with 5 subjects, and the error is always similar, I think it is unlikely to be a simple switch between subjects digitization (I double checked the origin of the files in any case)</div><div>it could be, however, a systematic error in the acquisition... But this system was successfully used with brainstorm, so I would not start with this hypothesis.</div></div></blockquote><div><br></div></span><div>I assume by this you mean the plots looked okay in BrainStorm, so we need to dig into it a bit.</div></div></div></div></blockquote><div><br></div><div>Yes</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 class="gmail_extra"><div class="gmail_quote"><div> </div></div></div></div></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><br></div><div>It's possible that BrainStorm projects the electrodes onto the scalp for visualization. </div></div></div></div></blockquote><div><br></div><div>I also think this was the case</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 class="gmail_extra"><div class="gmail_quote"><div>Do you have data from one subject you could share? If so, feel free to open an MNE-Python issue and we can work through it. </div></div></div></div></blockquote><div><br></div><div>I'll look for one example.</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 class="gmail_extra"><div class="gmail_quote"><div>For example, as a first pass you could look at the distribution histogram of the dig points in X and Y, and do the same thing for the MRI head surface coordinates. You can also look at the transformation matrix and ensure that it's a pure rotation + translation matrix, with no scaling (but it really should be!).</div></div></div></div></blockquote><div><br></div><div>It has to be, no? I never clicked the option to do scaling in the mne.gui.coregistration!</div><div>I'll check the histograms, also of the distances betweem electrodes and scalp (they seem to be quite constant, hence probably the elctrode height)</div><div><br></div><div>Thank you,</div><div>Leonardo</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 class="gmail_extra"><div class="gmail_quote"><span class="HOEnZb"><font color="#888888"><div><br></div><div>Eric</div><div><br></div><div> </div></font></span></div></div></div>
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