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<p style="margin-top:0;margin-bottom:0">Hey Eric,</p>
<p style="margin-top:0;margin-bottom:0">No, I've just used <span>label.morph() for each label from fsaverage to sample subject. </span></p>
<p style="margin-top:0;margin-bottom:0"><span>That is actually my question, if someone has a good approach to avoid these overlaps. </span></p>
<p style="margin-top:0;margin-bottom:0"><span>I'm using a naive approach (which also depends on the order of the labels) that uses a vertices->labels mapping:</span></p>
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<pre style="font-family: "DejaVu Sans Mono"; font-size: 11.3pt;"><span style="color:#000080;font-weight:bold;">for </span>label <span style="color:#000080;font-weight:bold;">in </span>labels:<br> <span style="color:#000080;font-weight:bold;">for </span>vertice <span style="color:#000080;font-weight:bold;">in </span>label.vertices:<br> lookup[hemi][vertice] = labels_names.index(label.name)</pre>
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<p style="margin-top:0;margin-bottom:0"><span>And then set the labels vertices:</span></p>
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<pre style="font-family: "DejaVu Sans Mono"; font-size: 11.3pt;"><span style="color:#000080;font-weight:bold;">for </span>vertice, label <span style="color:#000080;font-weight:bold;">in </span>lookup[hemi].items():<br> labels_vertices[label].append(vertice)</pre>
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<p style="margin-top:0;margin-bottom:0">I'm wondering if someone has implemented a better solution.</p>
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<p style="margin-top:0;margin-bottom:0">Thanks!</p>
<p style="margin-top:0;margin-bottom:0">Noam</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Eric Larson <larson.eric.d@gmail.com><br>
<b>Sent:</b> Monday, April 2, 2018 6:49:23 PM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] The problem with saving morphed labels to an annot file</font>
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<div>Hey Noam,</div>
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Does this code guarantee that the resulting morphed labels do not overlap?
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<div>Eric</div>
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<div class="x_gmail_extra"><br>
<div class="x_gmail_quote">On Mon, Apr 2, 2018 at 6:39 PM, Peled, Noam <span dir="ltr">
<<a href="mailto:NPELED@mgh.harvard.edu" target="_blank">NPELED@mgh.harvard.edu</a>></span> wrote:<br>
<blockquote class="x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<p style="margin-top:0; margin-bottom:0">Hey Alex,</p>
<p style="margin-top:0; margin-bottom:0">Yes, sure!</p>
<p style="margin-top:0; margin-bottom:0">You can find the code here:</p>
<p style="margin-top:0; margin-bottom:0"><a href="https://github.com/pelednoam/mmvt/blob/master/src/misc/labels_morphing_problem.py" class="x_m_-1325830981210329137OWAAutoLink" id="x_m_-1325830981210329137LPlnk21822" target="_blank">https://github.com/pelednoam/<wbr>mmvt/blob/master/src/misc/<wbr>labels_morphing_problem.py</a></p>
<p style="margin-top:0; margin-bottom:0">I'm using the <span>Lausanne125 parcellation <span>(<a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048121" class="x_m_-1325830981210329137OWAAutoLink" id="x_m_-1325830981210329137LPlnk412500" target="_blank">http://journals.<wbr>plos.org/plosone/article?id=<wbr>10.1371/journal.pone.0048121</a>),
but this problem can also be replicated using the <span>aparc.DKTatlas40 atlas (or almost any other atlas I assume).</span></span></span></p>
<p style="margin-top:0; margin-bottom:0"><span>If you wish to run it with the <span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">Lausanne125
parcellation, the fsaverage annot files can be found here:</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span><a href="https://www.dropbox.com/sh/qvpvzf35konkwe5/AADVCp24TxLa_SBUSAAvCuFMa?dl=0" class="x_m_-1325830981210329137OWAAutoLink" id="x_m_-1325830981210329137LPlnk973285" target="_blank">https://www.dropbox.com/sh/<wbr>qvpvzf35konkwe5/AADVCp24TxLa_<wbr>SBUSAAvCuFMa?dl=0</a></span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>Thanks!</span></p>
<p style="margin-top:0; margin-bottom:0"><span>Noam</span><br>
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<div id="x_m_-1325830981210329137divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b>
<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.<wbr>harvard.edu</a> <<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.<wbr>harvard.edu</a>> on behalf
of Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>><br>
<b>Sent:</b> Wednesday, March 28, 2018 3:32:34 AM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] The problem with saving morphed labels to an annot file</font>
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<div class="x_m_-1325830981210329137PlainText">hi Noam,<br>
<br>
I personally don't have a solution for this. Maybe someone else?<br>
<br>
could you provide a code snippet to replicate the pb?<br>
<br>
Alex<br>
<br>
<br>
On Wed, Mar 28, 2018 at 4:24 AM, Peled, Noam <<a href="mailto:NPELED@mgh.harvard.edu" target="_blank">NPELED@mgh.harvard.edu</a>> wrote:<br>
> Dear group,<br>
><br>
> It seems like an old problem, but I couldn't find a reasonable solution,<br>
><br>
> When morphing labels from fsaverage to a subject, in most cases the annot<br>
> file cannot be written due to vertices that belong to more than one label.<br>
><br>
> I've implemented several solutions, but in some cases, none of them gives a<br>
> reasonable result.<br>
><br>
><br>
> Thanks,<br>
><br>
> Noam<br>
><br>
><br>
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