[Neuroimaging] [pysurfer] making background brain more transparent

[Kirstie Whitaker]

Sorry - Basically I want to just make the background brain stand out a
little less in my figures so what I'd hoped was that it would be possible
to simple "fade out" the background brain (not my ROI overlays) a little.

If I were showing a slice in matplotlib I'd do something like this:

import  numpy as np
import matplotlib.pylab as plt
a = np.random.rand(100,100)
plt.imshow(a, alpha=0.5, cmap='gray')
plt.show()

(with maybe a being my brain slice rather than just random numbers)

Sorry I wasn't clear - does that help??

Kx

On 31 July 2015 at 15:54, Michael Waskom <mwaskom at stanford.edu> wrote:

> Hi Kristie,
>
> I think I'm a bit confused about your question. What do you mean make it
> *more* transparent? As far as I know, the brain geometry is drawn at full
> opacity so I might not understand what you are trying to do.
>
> Best,
> Michael
>
> On Fri, Jul 31, 2015 at 3:00 AM, Kirstie Whitaker <kw401 at cam.ac.uk> wrote:
>
>> Hi everyone,
>>
>> I'd like to make the background brain in pysurfer a little more
>> transparent, so I'm looking for an "alpha" flag or something similar. I
>> don't think this yet exists according to the documentation on changing
>> the curvature color scheme
>> <http://pysurfer.github.io/documentation/custom_viz.html#changing-the-curvature-color-scheme>
>> but I wonder if anyone has a hack that I could implement?
>>
>> An alternative to the alpha parameter would be to create a fifth
>> (personalised) color scheme perhaps?
>>
>> Thanks!
>> (This is also a question on neurostars.org
>> <http://neurostars.org/p/3315/> if anyone wants to answer there instead!)
>>
>> Kx
>>
>> --
>> 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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>>
>>
>
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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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