<div dir="ltr">hi <span style="color:rgb(0,0,0);font-size:12.8px">Talitha,</span><div><span style="color:rgb(0,0,0);font-size:12.8px"><br></span></div><div><span style="color:rgb(0,0,0);font-size:12.8px">ok so it's a mayavi install problem and not a bug on the mne side.</span></div><div><span style="color:rgb(0,0,0);font-size:12.8px"><br></span></div><div><span style="color:rgb(0,0,0);font-size:12.8px">you should report this issue on the mayavi issue tracker:</span></div><div><span style="color:rgb(0,0,0);font-size:12.8px"><br></span></div><div><font color="#000000"><span style="font-size:12.8px"><a href="https://github.com/enthought/mayavi/issues">https://github.com/enthought/mayavi/issues</a></span></font><br></div><div><font color="#000000"><span style="font-size:12.8px"><br></span></font></div><div><font color="#000000"><span style="font-size:12.8px">I assume you followed the install instructions we provide:</span></font></div><div><font color="#000000"><span style="font-size:12.8px"><br></span></font></div><div><font color="#000000"><span style="font-size:12.8px"><a href="http://martinos.org/mne/dev/install_mne_python.html#install-a-python-interpreter-and-dependencies">http://martinos.org/mne/dev/install_mne_python.html#install-a-python-interpreter-and-dependencies</a></span><br></font></div><div><font color="#000000"><span style="font-size:12.8px"><br></span></font></div><div><font color="#000000"><span style="font-size:12.8px">hope this helps</span></font></div><div><font color="#000000"><span style="font-size:12.8px"><br></span></font></div><div><font color="#000000"><span style="font-size:12.8px">Alex</span></font></div><div><font color="#000000"><span style="font-size:12.8px"><br></span></font></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Jun 11, 2017 at 10:47 AM, Talitha Ford <span dir="ltr"><<a href="mailto:tcford@swin.edu.au" target="_blank">tcford@swin.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Alex,
<div>I can import lab fine, but mlab.test_mesh() opens the TVTK window and then freezes (with the Mac pinwheel). As before, hitting ctrl+D displays the image in the TVTK window, but it’s not interactive at all. I hope that makes sense,</div>
<div><br>
</div>
<div>Thanks,</div>
<div>
<div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div>
<div style="word-wrap:break-word">
Talitha<br>
<br>
</div><div><div class="h5">
<div style="word-wrap:break-word">
On 11 Jun 2017, at 17:21, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-<wbr>paristech.fr</a>> wrote:</div>
</div></div></div>
</div>
</div>
</div><div><div class="h5">
<div><br class="m_9064457291918066820Apple-interchange-newline">
<div>
<div dir="ltr">hi Talitha,
<div><br>
</div>
<div>can you just confirm that mayavi without mne works. You can test with</div>
<div><br>
</div>
<div>
<div>from mayavi import mlab</div>
<div>mlab.test_mesh()<br>
</div>
</div>
<div><br>
</div>
<div>ALex</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Jun 11, 2017 at 6:35 AM, Talitha Ford <span dir="ltr">
<<a href="mailto:tcford@swin.edu.au" target="_blank">tcford@swin.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Alex,
<div>Sorry for the delay. No, when I read in the source estimate that results from applying the inverse and attempt to plot it, the TVTK window opens but no image appears unless I ctrl+D to exit ipython. Here are the lines of code I use:</div>
<span><br>
</span><span>import mne<br>
from mne.source_estimate impor<wbr>t SourceEstimate<br>
</span><span>stc = mne.read_source_estimate('OB86<wbr>0_stand2_mne_dSPM_inv-lh.stc')<br>
</span><span>stc.plot("fsaverage")</span><span><br>
<br>
</span>
<div>Thanks for your help,</div>
<div><br>
<div>
<div style="word-wrap:break-word">
<div style="word-wrap:break-word">
<div>
<div style="word-wrap:break-word">Talitha </div>
</div>
</div>
</div>
</div>
</div>
<div>
<div class="m_9064457291918066820h5"><br>
<div>
<div>On 6 Jun 2017, at 19:19, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-pa<wbr>ristech.fr</a>> wrote:</div>
<br class="m_9064457291918066820m_-3709117089227510251Apple-interchange-newline">
<div>
<div dir="ltr">hi <span style="font-size:12.8px">Talitha,</span>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">does your mayavi setup works otherwise? can you do stc.plot with the output of dSPM/MNE apply_inverse?</span></div>
<div><span style="font-size:12.8px">In other words is it a mayavi/vtk problem or an mne/pysurfer problem?</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Alex</span></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jun 6, 2017 at 2:54 AM, Talitha Ford <span dir="ltr">
<<a href="mailto:tcford@swin.edu.au" target="_blank">tcford@swin.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="white" lang="EN-GB" link="#0563C1" vlink="#954F72">
<div class="m_9064457291918066820m_-3709117089227510251m_5205675051517235788WordSection1">
<p class="MsoNormal"><span lang="EN-AU">Dear list,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-AU"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-AU">I am attempting to run the </span>
‘2 samples permutation test on source data with spatio-temporal clustering’ tutorial (<a href="https://martinos.org/mne/stable/auto_tutorials/plot_stats_cluster_spatio_temporal_2samp.html" target="_blank">https://martinos.org/mne/stab<wbr>le/auto_tutorials/plot_stats_c<wbr>luster_spatio_temporal_2samp.h<wbr>tml</a>),
but when I get to visualising the SourceEstimate object, a <span lang="EN-AU">
TVTK window opens and freezes; no image appears and I am unable to close the window without terminating the iPython session. Also, stc.resample(50) throws an error ‘</span>ImportError: cannot import name sigtools’<u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-AU"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-AU">I am running iPython version 2.7 from the Anaconda distribution, and have up-to-date mne, scipy, PySurfer,
</span>matplotlib, scikit-learn and mayavi packages. I am running the analysis on an iMac OS Sierra 10.12.5.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Can someone please point me in the right direction to overcome this?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you,<u></u><u></u></p>
<p class="MsoNormal">Talitha<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-AU"><u></u> <u></u></span></p>
</div>
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