[Neuroimaging] [pysurfer] making background brain more transparent

Kirstie Whitaker kw401 at cam.ac.uk
Fri Jul 31 19:19:34 CEST 2015

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!


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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