<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span></p><p></p><div dir="ltr"><div dir="ltr">Thanks Josh,<div>I tried changing the n_lines parameter in the plot_connectivity_circle() function, it reduces the connections only. It still shows weak connections or connections below desired value. I&#39;ll try other way you mentioned.</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 28, 2019 at 11:57 PM Bear, Joshua &lt;<a href="mailto:JOSHUA.BEAR@ucdenver.edu">JOSHUA.BEAR@ucdenver.edu</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word">Hi Vivek, <div><br></div><div>In those examples, I believe the thresholding occurs from the n_lines parameter in the plot_connectivity_circle() function. n_lines=300 means that only the 300 strongest connections are plotted. See the documentation for plot_connectivity_circle: <a href="https://martinos.org/mne/stable/generated/mne.viz.plot_connectivity_circle.html#mne.viz.plot_connectivity_circle" target="_blank">https://martinos.org/mne/stable/generated/mne.viz.plot_connectivity_circle.html#mne.viz.plot_connectivity_circle</a></div><div><br></div><div>If you wanted finer control over the threshold, you would need to either manipulate the values of the CON output (array) directly, or calculate an n_lines threshold that would capture your desired range. For example, if you wanted only those connections with a value &gt; 0.3, you could count the number of connections with value &gt; 0.3 and then use that number for your n_lines value. (I think this would work properly but have not tried it myself, so there might be some nuances to troubleshoot.)</div><div><br></div><div>It wasn’t clear to me whether you meant significant connections or just an absolute value. The above suggestions threshold based on absolute value. You could use some statistical test appropriate for your own data to determine the absolute value, but depending on your goal and data there might be more direct methods. </div><div><br></div><div>Cheers,</div><div>Josh</div><div><br></div><div><br><div>
<div dir="auto" style="word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy</div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">University of Colorado and Children’s Hospital Colorado<br>13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285 </div><br class="gmail-m_488117676827002254Apple-interchange-newline"></div><br class="gmail-m_488117676827002254Apple-interchange-newline">
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<div><br><blockquote type="cite"><div>On Feb 28, 2019, at 2:18 AM, Vivek Sharma &lt;<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>&gt; wrote:</div><br class="gmail-m_488117676827002254Apple-interchange-newline"><div><p style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)">        External Email - Use Caution        </span></p><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br class="gmail-m_488117676827002254webkit-block-placeholder"></div><div dir="ltr" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">By significant connections I also mean the strongest connections. How to keep a threshold to remove weak connections.</div><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div class="gmail_quote" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div dir="ltr" class="gmail_attr">On Wed, Feb 27, 2019 at 11:08 AM Vivek Sharma &lt;<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Marijn,</div><div>Its a single subject MEG data.</div><div>By significant I mean, if you look at the figure in the following example:</div><div><a href="https://martinos.org/mne/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py" target="_blank">https://martinos.org/mne/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py</a><br></div><div>on lower right, it shows a bar that display the strength of those connections with values 0.4-0.6. When I plot for my data the bar displays values from 0.15-0.20 and shows the connections below 0.15 also. How can I restrict it to show only connections above 0.15?</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Feb 26, 2019 at 6:17 PM Marijn van Vliet &lt;<a href="mailto:w.m.vanvliet@gmail.com" target="_blank">w.m.vanvliet@gmail.com</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">        External Email - Use Caution       <span class="gmail-m_488117676827002254Apple-converted-space"> </span><br><br>Dear Vivek,<br><br>significant in what way? If you have multiple subjects, you can compute a t-statistic for each connection. If you have multiple experimental conditions, you can do a paired t-test between conditions…. Could you tell us a bit more about the data?<br><br>best,<br>Marijn.<br><br>&gt; On 26 Feb 2019, at 10:01, Vivek Sharma &lt;<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>&gt; wrote:<br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt;         External Email - Use Caution       <span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt; I&#39;m using the following example code to compute connectivity.<br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><a href="https://martinos.org/mne/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py" rel="noreferrer" target="_blank">https://martinos.org/mne/stable/auto_examples/connectivity/plot_mne_inverse_label_connectivity.html#sphx-glr-auto-examples-connectivity-plot-mne-inverse-label-connectivity-py</a><br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt; How can I apply statistical threshold to have only significant connections?<br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt; --<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br>&gt; Vivek Sharma<br>&gt; _______________________________________________<br>&gt; Mne_analysis mailing list<br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>&gt;<span class="gmail-m_488117676827002254Apple-converted-space"> </span><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br><br><br>_______________________________________________<br>Mne_analysis mailing list<br><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div><br clear="all"><div><br></div>--<span class="gmail-m_488117676827002254Apple-converted-space"> </span><br><div dir="ltr" class="gmail-m_488117676827002254gmail-m_1676277217495259021gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-size:12.8px">Vivek Sharma</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></blockquote></div><br clear="all" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br></div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">--<span class="gmail-m_488117676827002254Apple-converted-space"> </span></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div dir="ltr" class="gmail-m_488117676827002254gmail_signature" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-size:12.8px">Vivek Sharma</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">_______________________________________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Mne_analysis mailing list</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none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Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><span style="font-size:12.8px">Vivek Sharma</span></div></div></div></div></div></div></div></div></div></div></div></div></div></div>