<div dir="ltr">Thanks very much</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 23, 2015 at 3:29 PM, Eric Larson <span dir="ltr"><<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@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">The morph matrix is linear in terms of the superpositions of signals that end up on any given vertex. It doesn't mean that point 1 on surface A maps to point 1 on surface B, though, or imply anything about how the spatial connectivity of surface A relates to that of B. So you do have to recompute/use the connectivity for surface B. In my pipeline that just means having one connectivity matrix -- that for fsaverage, since that's where all the data end up.<span class="HOEnZb"><font color="#888888"><div><br></div><div>Eric</div></font></span><div><div class="h5"><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 23, 2015 at 4:33 AM, Rezvan Farahi <span dir="ltr"><<a href="mailto:rezvan.farahi@gmail.com" target="_blank">rezvan.farahi@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">Hi,<div><br></div><div>One question following Eric's explanations regarding data morphing.</div><div>So far in my analyses, my understanding was that I can do morphing just before group analysis (i.e. after computing connectivity). And as Eric said since morphing procedure is something linear I assumed there is no difference if I first morph source signals then compute connectivity or the other way around</div><div><br></div><div>But both Denis and Matthias suggested data morphing before connectivity. Does it mean that it would introduce any biases if I compute it the other way around?</div><div><br></div><div>Many thanks,</div><div>Rezvan</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 23, 2015 at 1:53 AM, Eric Larson <span dir="ltr"><<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@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">Hey Per,<div><br></div><div>There are two different "morph" operations being talked about.</div><div><br></div><div>I have never morphed source spaces, but this is my understanding of how it works. Morphing source spaces means taking the subset of vertices from subject's A's brain mesh (typically white) that are in that subject's existing source space, and finding the vertices for subject B that are as close as possible based on A and B's spherical coregistration / morph map. In other words, the source space for subject B is created by subsampling subject B's high density cortical mesh vertices using the spherical-morphing correspondence of subject A's subsampled mesh. In physical space, the vertices from subject A could thus be in very different positions from their counterparts for subject B, but conceptually each vertex from subject A is intended to be in an equivalent anatomical location in subject B. Since subject A's source space was originally subdivided in a way that to some extent evenly subsampled its physical space, the differences in cortical folding between subjects A and B may result in subject B's (morphed) source space vertices having a spacing that is less uniform than a source space that was created for subject B directly. In this scheme, data does not need to be morphed between one subject and another, because the vertices in their source spaces are the same, anatomically speaking.</div><div><br></div><div>The other type of morphing is the one I talked about, data morphing. This is required when subject A has some source space created for it using any subsampling, and subject B has a source space created for it with any subsampling independently. The vertices from subject A were created independently from those in subject B (e.g., vertex 1 in A might map to 1093 in B, and 1093 in A might map to 5921 in B, etc.) There is a morphing procedure that allows you to map activity (i.e., source estimates) from subject A to subject B or vice-versa via a linear transformation. This transformation also makes use of the morph maps / spherical anatomical alignment of A and B, but it uses a smudging-like procedure to effectively push data from one subsampled mesh onto the other. This is also detailed in the manual somewhere. This is the procedure I am most familiar with -- create source space for each subject, arrive at source estimates for each subject in their own space, and for group analyses, use mne-python or MNE-C to morph all subjects' data to fsaverage's ico-5 source space for analysis.</div><div><br></div><div>Cheers,</div><div>Eric</div><div><br></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 22, 2015 at 4:40 PM, Denis-Alexander Engemann <span dir="ltr"><<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@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">To elaborate on my note, this is what I do exactly to deal with this:<div><br></div><div><a href="https://gist.github.com/dengemann/f90cf354816273fe87eb" target="_blank">https://gist.github.com/dengemann/f90cf354816273fe87eb</a><br></div><div><br></div><div>It's a genarator function that you can pass to `mne.connectivity.spectral_connectivity`</div><div><br></div><div>Hope this is useful for you,</div><div><br></div><div>Denis</div><div><div>
<div class="gmail_extra"><br><div class="gmail_quote">2015-04-23 0:30 GMT+02:00 Per Arnold Lysne <span dir="ltr"><<a href="mailto:lysne@unm.edu" target="_blank">lysne@unm.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello All,<br>
<br>
Apologies for belaboring this thread - and thanks for everyone's useful comments. It appears that I may not understand the morphing option in mne_setup_source_space as well as I thought.<br>
<br>
I understand Matthias' original point of wanting to analyze individual subjects' in a common, "canonical" source space. I had assumed that, when morphing was done in mne_setup_source_space (i.e. --subject MySubject --morph fsaverage), a common space would be the result (the fsaverage space) and that the forward and inverse operators would be adjusted to compensate for the changed cortical surface. In other words, there would be no loss of accuracy and that fsaverage would be the new, common source space. Am I missing something?<br>
<br>
In reviewing the 2.7.3 manual I see a comment, "The drawback of this approach is that the spacing between source locations in the “morph” subject is not going to be as uniform as it would be without morphing" (under --morph, p22). Does this mean that the original subject's vertices are not being translated directly to those on fsaverage? In other words, although the new morphed surface may match fsaverage, there is not a common set of vertices shared between them?<br>
<br>
(This complicates things for me because I am working on a group localization and am expecting the morphed individual subjects to have a common number of vertices in comparable locations.)<br>
<br>
Thanks again,<br>
<span><br>
Per Lysne<br>
University of New Mexico<br>
<br>
</span>________________________________________<br>
From: <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a> <<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>> on behalf of Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-paristech.fr</a>><br>
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To: Discussion and support forum for the users of MNE Software<br>
Subject: Re: [Mne_analysis] mne_setup_source_space with --morph option => morphing fsaverage onto subject<br>
<div><div><br>
hi Matthias,<br>
<br>
what you do makes sense and I would do the same.<br>
<br>
Not sure what's going wrong here. Maybe somebody has time<br>
to look at this problem with the triangles.<br>
<br>
Alex<br>
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