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Hi Alex,
<div class="">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 class=""><br class="">
</span><span class="">import mne<br class="">
from mne.source_estimate import SourceEstimate<br class="">
</span><span class="">stc = mne.read_source_estimate('OB860_stand2_mne_dSPM_inv-lh.stc')<br class="">
</span><span class="">stc.plot("fsaverage")</span><span class=""><br class="">
<br class="">
</span>
<div class="">Thanks for your help,</div>
<div class=""><br class="">
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<div class="" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
Talitha </div>
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<div>
<div class="">On 6 Jun 2017, at 19:19, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr" class="">alexandre.gramfort@telecom-paristech.fr</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">hi <span style="font-size:12.8px" class="">Talitha,</span>
<div class=""><span style="font-size:12.8px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8px" class="">does your mayavi setup works otherwise? can you do stc.plot with the output of dSPM/MNE apply_inverse?</span></div>
<div class=""><span style="font-size:12.8px" class="">In other words is it a mayavi/vtk problem or an mne/pysurfer problem?</span></div>
<div class=""><span style="font-size:12.8px" class=""><br class="">
</span></div>
<div class=""><span style="font-size:12.8px" class="">Alex</span></div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Tue, Jun 6, 2017 at 2:54 AM, Talitha Ford <span dir="ltr" class="">
<<a href="mailto:tcford@swin.edu.au" target="_blank" class="">tcford@swin.edu.au</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span lang="EN-AU" class="">Dear list,<u class=""></u><u class=""></u></span></p>
<p class="MsoNormal"><span lang="EN-AU" class=""><u class=""></u> <u class=""></u></span></p>
<p class="MsoNormal"><span lang="EN-AU" class="">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" class="">https://martinos.org/mne/<wbr class="">stable/auto_tutorials/plot_<wbr class="">stats_cluster_spatio_temporal_<wbr class="">2samp.html</a>),
but when I get to visualising the SourceEstimate object, a <span lang="EN-AU" class="">
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 class=""></u><u class=""></u></p>
<p class="MsoNormal"><span lang="EN-AU" class=""><u class=""></u> <u class=""></u></span></p>
<p class="MsoNormal"><span lang="EN-AU" class="">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 class=""></u><u class=""></u></p>
<p class="MsoNormal"><u class=""></u> <u class=""></u></p>
<p class="MsoNormal">Can someone please point me in the right direction to overcome this?<u class=""></u><u class=""></u></p>
<p class="MsoNormal"><u class=""></u> <u class=""></u></p>
<p class="MsoNormal">Thank you,<u class=""></u><u class=""></u></p>
<p class="MsoNormal">Talitha<u class=""></u><u class=""></u></p>
<p class="MsoNormal"><u class=""></u> <u class=""></u></p>
<p class="MsoNormal"><span lang="EN-AU" class=""><u class=""></u> <u class=""></u></span></p>
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