[Neuroimaging] Pysurfer Brain's save_image method produces images with only background color

John Pellman pellman.john at gmail.com
Tue Sep 13 13:24:23 EDT 2016

It looks like it might be related to the following issue described at


On Mon, Sep 12, 2016 at 2:00 PM, John Pellman <pellman.john at gmail.com>

> Hi all,
> I'm encountering a peculiar Pysurfer error on our server and I was
> wondering if anyone has encountered anything similar or might have some
> insight into how I can tackle it.  Basically, when our researchers try to
> save a png image using Brain.save_image() or Brain.save_imageset() the
> images produced only contain the background color (as you may have inferred
> from the subject line).  I've traced this back to Scipy method
> (scipy.misc.imsave), but it looks like this would only output an empty png
> if the image passed in were completely zeroed out.  Our setup uses the
> following versions of pysurfer/its dependencies:
> Numpy: 1.10.0.dev0+1fe98ff
> Scipy: 0.17.0.dev0+f2f6e48
> Ipython: 3.1.0
> nibabel: 2.0.0
> Mayavi: 4.4.2
> matplotlib: 1.4.3
> PIL: 1.1.7
> Pysurfer: 0.5
> This setup is running within a Miniconda environment using Python 2.7.11.
> I'm uncertain if this is related, but running the example code here
> <http://pysurfer.github.io/examples/plot_basics.html> produces the
> following warning:
> *(ipython:20765): Gdk-WARNING **:
> /build/buildd/gtk+2.0-2.24.27/gdk/x11/gdkdrawable-x11.c:952 drawable is not
> a pixmap or window*
> Any insight would be greatly appreciated.
> Best,
> John Pellman
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