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

John Pellman pellman.john at gmail.com
Mon Sep 12 14:00:20 EDT 2016


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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