<div dir="ltr"><div class="gmail_default" style="font-size:small">Hi Alex,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Thanks for your reply! I did:</div><div class="gmail_default" style=""><pre style="font-size:12pt;background-color:rgb(255,255,255);color:rgb(0,0,0);font-family:"Courier New"">surf = fwd[<span style="color:rgb(0,128,0);font-weight:bold">'src'</span>][hemi_idx]<br>tris = surf[<span style="color:rgb(0,128,0);font-weight:bold">'use_tris'</span>] <span style="color:rgb(128,128,128);font-style:italic"><br></span></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><pre style="font-size:12pt;font-family:"Courier New";background-color:rgb(255,255,255);color:rgb(0,0,0)"><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0);font-family:"Courier New";font-size:12pt"><span style="background-color:rgb(255,228,255)">edges</span> = mesh_edges(tris)</pre></pre><font face="arial, helvetica, sans-serif" style="">The dimensions of 'edges' are 642*642 in my case. </font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">I'm not sure I understand how coo_matrix in the mesh_edges function works. </font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">I saw that in the mesh_edges function,</font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style=""><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0);font-family:"Courier New";font-size:12pt">npoints = np.max(tris) + <span style="color:rgb(0,0,255)">1 </span></pre>Which gives one extra point.</font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">Then:</font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style=""><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0);font-family:"Courier New";font-size:12pt">edges = coo_matrix((ones_ntris, (x, y)), <span style="color:rgb(102,0,153)">shape</span>=(npoints, npoints))</pre>Which I interpreted as adding a '1' at element (x[i],y[i]) of 'edges' each time (x[i],y[i]) appears in (x,y), like in <a href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.coo_matrix.html">this example on constructing a matrix using ijv format</a>.</font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">However, since the largest element of 'tris' is np.max(tris), why are there nonzero entries for the (np.max(tris) + 1)th row/col in the 'edges' matrix?</font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">Should I be using edges[0:npoints-1,0:npoints-1] as my adjacency matrix? </font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style=""><br></font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">Thanks and Best,</font></pre><pre style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><font face="arial, helvetica, sans-serif" style="">Gladia</font></pre><br></div><div class="gmail_default" style="font-size:small"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Mar 4, 2018 at 3:29 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</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">i suppose you mean use_tris with _<div><br></div><div>it's normal to have twice more triangles than vertices.<div><br></div><div>see for example here:</div><div><br></div><div><a href="https://github.com/mne-tools/mne-python/blob/master/mne/viz/_3d.py#L1444" target="_blank">https://github.com/mne-tools/<wbr>mne-python/blob/master/mne/<wbr>viz/_3d.py#L1444</a><br></div><div><br></div><div>how we get the triangles in low resolution with vertices index that go</div><div>from 0 to 581 in your case.</div><div><br></div><div>HTH</div><div>Alex</div><div><br></div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 3, 2018 at 10:58 PM, Gladia Hotan <span dir="ltr"><<a href="mailto:gladiach@gmail.com" target="_blank">gladiach@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 class="gmail_default" style="font-size:small">Hi Alex,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">I'm still not sure how to get the adjacency matrix, based on the example. It seems like lh_faces and rh_faces contain the faces from the original cortical parcellation, before some sources are removed? I have an ico 3 source space. My leadfield matrix has 1162 sources in total. Thus fwd['src'][0]['vertno'].shape = 581 and <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">fwd['src'][1]['vertno'].sh<wbr>ape = 581. However, <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">fwd['src'][0]['usetri<wbr>s'].shape = 1280 and <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">fwd['src'][1]['usetris']</span>.shape = 1280, so I'm not sure which faces correspond to which vertices?</span></span></div><div class="gmail_default" style="font-size:small"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><br></span></span></div><div class="gmail_default" style="font-size:small"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">Thanks and Best,<br>Gladia</span></span></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_8272461268463871713h5">On Tue, Feb 6, 2018 at 5:26 AM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_8272461268463871713h5">This is the old script I was pointing to:<br>
<br>
<a href="https://github.com/mne-tools/mne-python/blob/maint/0.4/examples/plot_read_forward.py" rel="noreferrer" target="_blank">https://github.com/mne-tools/m<wbr>ne-python/blob/maint/0.4/examp<wbr>les/plot_read_forward.py</a><br>
<br>
HTH<br>
Alex<br></div></div>
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