[Neuroimaging] [pysurfer] making background brain more transparent

Michael Waskom mwaskom at stanford.edu
Fri Aug 7 17:19:07 CEST 2015

Hi Kristie,

Just wanted to follow up on this. I assume you figured it out yourself, but
in case anyone finds this thread while searching, we've released 0.6 and
the documentation has two relevant examples:

http://pysurfer.github.io/examples/plot_label_foci.html (shows how to pass
custom parameters to the binarized curvature)
http://pysurfer.github.io/examples/plot_probabilistic_label.html (shows how
to use a continuous map of curvature)


On Fri, Jul 31, 2015 at 10:19 AM, Kirstie Whitaker <kw401 at cam.ac.uk> wrote:

> Ah yes - very good point - I hadn't thought about the "see through" effect
> of changing the alpha parameter.
> I'll grab the development version and see if there are any parameters that
> my boss likes better than the classic ;)
> Thanks Michael and Vanessa for the suggestions!
> Kx
> On 31 July 2015 at 18:15, Michael Waskom <mwaskom at stanford.edu> wrote:
>> Hi Kristie,
>> If you decrease the alpha value of the anatomy mesh, you'll be able to
>> see through it. While this can be useful for "glass brain" type volume
>> visualizations, it's probably not going to give you the effect you want for
>> showing surface-based ROIs, as it will just be hard to tell what you're
>> looking at (in my experience). For that reason, alpha isn't exposed as a
>> parameter. I would say though that the development version of pysurfer lets
>> you pass custom parameters for the colormap used to show the curvature (in
>> binary or continuous values) so you could play around with that to see if
>> you can find something that deemphasizes the anatomy. You can also plot
>> with curv=False, of course, but that makes it harder to understand where
>> the ROIs are.
>> Hope that helps,
>> Michael
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> --
> Kirstie Whitaker, PhD
> Research Associate
> Department of Psychiatry
> University of Cambridge
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
> *Phone: *+44 7583 535 307
> *Website:* www.kirstiewhitaker.com
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