[Mne_analysis] SourceEstimate.plot() fail

[Alexandre Gramfort]

hi Talitha,

ok so it's a mayavi install problem and not a bug on the mne side.

you should report this issue on the mayavi issue tracker:

https://github.com/enthought/mayavi/issues

I assume you followed the install instructions we provide:

http://martinos.org/mne/dev/install_mne_python.html#install-a-python-interpreter-and-dependencies

hope this helps

Alex


On Sun, Jun 11, 2017 at 10:47 AM, Talitha Ford <tcford at swin.edu.au> wrote:

> Hi Alex,
> 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,
>
> Thanks,
> Talitha
>
> On 11 Jun 2017, at 17:21, Alexandre Gramfort <alexandre.gramfort at telecom-
> paristech.fr> wrote:
>
> hi Talitha,
>
> can you just confirm that mayavi without mne works. You can test with
>
> from mayavi import mlab
> mlab.test_mesh()
>
> ALex
>
>
> On Sun, Jun 11, 2017 at 6:35 AM, Talitha Ford <tcford at swin.edu.au> wrote:
>
>> Hi Alex,
>> 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:
>>
>> import mne
>> from mne.source_estimate import SourceEstimate
>> stc = mne.read_source_estimate('OB860_stand2_mne_dSPM_inv-lh.stc')
>> stc.plot("fsaverage")
>>
>> Thanks for your help,
>>
>> Talitha
>>
>> On 6 Jun 2017, at 19:19, Alexandre Gramfort <
>> alexandre.gramfort at telecom-paristech.fr> wrote:
>>
>> hi Talitha,
>>
>> does your mayavi setup works otherwise? can you do stc.plot with the
>> output of dSPM/MNE apply_inverse?
>> In other words is it a mayavi/vtk problem or an mne/pysurfer problem?
>>
>> Alex
>>
>> On Tue, Jun 6, 2017 at 2:54 AM, Talitha Ford <tcford at swin.edu.au> wrote:
>>
>>> Dear list,
>>>
>>>
>>>
>>> I am attempting to run the ‘2 samples permutation test on source data
>>> with spatio-temporal clustering’ tutorial (https://martinos.org/mne/stab
>>> le/auto_tutorials/plot_stats_cluster_spatio_temporal_2samp.html), but
>>> when I get to visualising the SourceEstimate object, a 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 ‘ImportError: cannot import name sigtools’
>>>
>>>
>>>
>>> I am running iPython version 2.7 from the Anaconda distribution, and
>>> have up-to-date mne, scipy, PySurfer, matplotlib, scikit-learn and
>>> mayavi packages. I am running the analysis on an iMac OS Sierra 10.12.5.
>>>
>>>
>>>
>>> Can someone please point me in the right direction to overcome this?
>>>
>>>
>>>
>>> Thank you,
>>>
>>> Talitha
>>>
>>>
>>>
>>>
>>>
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