mne.viz.plot_source_estimates generates a blank window

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1

Hi, I ran mne.viz.plot_source_estimates(stc,subject=<subject_name>,...) but
I got a blank window and this error:

(<unknown>:39799): Gtk-WARNING **: gtk_disable_setlocale() must be called
before gtk_init()
Traceback (most recent call last):
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.py",
line 3035, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-1-16aa827441a7>", line 1, in <module>

mne.viz.plot_source_estimates(stc,subject='eeganes03',surface='inflated',hemi='lh',colormap='auto',time_label='time=%0.2fms',smoothing_steps=10,transparent=None,alpha=1.0,time_viewer=False,config_opts=None,subjects_dir=None,figure=None,views='lat',colorbar=True,clim='auto')
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mne/viz/_3d.py",
line 593, in plot_source_estimates
    brain = Brain(subject, hemi, surface, **kwargs)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/surfer/viz.py",
line 395, in __init__
    self._scene_size, offscreen)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/surfer/viz.py",
line 212, in _make_viewer
    figure = mlab.figure(title, size=(w, h))
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/tools/figure.py",
line 86, in figure
    engine.new_scene(name=name, size=size)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/apptools/scripting/recordable.py",
line 45, in _wrapper
    result = func(*args, **kw)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/core/engine.py",
line 434, in new_scene
    viewer = self.scene_factory(**factory_kwargs)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/core/ui/mayavi_scene.py",
line 89, in viewer_factory
    viewer.open()
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/pyface/i_window.py",
line 145, in open
    self._create()
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/pyface/ui/wx/application_window.py",
line 151, in _create
    contents = self._create_contents(body)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/tools/ivtk.py",
line 392, in _create_contents
    self.scene = self._scene_factory(parent)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/mayavi/core/ui/mayavi_scene.py",
line 68, in mayavi_scene_factory
    s = MayaviScene(parent, stereo=p['stereo'])
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/decorated_scene.py",
line 69, in __init__
    super(DecoratedScene, self).__init__(parent, **traits)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/scene.py",
line 302, in __init__
    super(Scene, self).__init__(parent, **traits)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/tvtk_scene.py",
line 201, in __init__
    self.control = self._create_control(parent)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/decorated_scene.py",
line 103, in _create_control
    self._panel)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/scene.py",
line 575, in _create_control
    stereo=self.stereo)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/tvtk/pyface/ui/wx/wxVTKRenderWindowInteractor.py",
line 186, in __init__
    attribList=attribList)
  File
"/usr/pubsw/packages/python/anaconda/lib/python2.7/site-packages/wx-3.0-gtk2/wx/glcanvas.py",
line 106, in __init__
    _glcanvas.GLCanvas_swiginit(self,_glcanvas.new_GLCanvas(*args,
**kwargs))
TypeError: Argument given by name ('attribList') and position (3)

I get the same error whether or not I set the 'SUBJECT' environment
variable (using os.environ['SUBJECT']=<subject_name>. Could anyone tell me
how to get around this?

Best,
Gladia
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2

Oh, this does not look nice. Does anybody have experience with Mayavi on
Windows? Eric?

3

Is this on Windows? That looks like a Unix directory structure to me.

In any case, it looks like a bug with Anaconda to me. It will probably be
tough to debug. If you can make an mne-python issue, we can try to isolate
it to some minimal example that only uses Mayavi. Then the Anaconda folks
can fix it hopefully.

In the meantime, do you know if your packages are up to date? You can
normally do e.g. `conda update mayavi` but it looks like you're on a site
install, so you'll have to ask your IT folks (and maybe see if they can
replicate it, too).

Eric

4

My bad, Eric, it's Linux.

5

Hi,

This is on Linux.

Sure, should I post the error on github?

I'm quite new to python so I don't know how to check if my packages are up
to date. I'm using the python package installed on the cluster at the
Martinos center. I'll check with the IT folks, thanks!

Best,
Gladia

6

Yeah go ahead and make an issue, we'll try to isolate the problem there.

Eric