SourceEstimate.plot() fail

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1

Dear list,

I am attempting to run the ?2 samples permutation test on source data with spatio-temporal clustering? tutorial (https://martinos.org/mne/stable/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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2

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

3

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

4

hi Talitha,

can you just confirm that mayavi without mne works. You can test with

from mayavi import mlab
mlab.test_mesh()

ALex

5

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

6

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

7

Thanks Alex,

Yes, I followed the MNE installation instructions. I?ll log the issue with mayavi.

Cheers,
Talitha Ford