-
Notifications
You must be signed in to change notification settings - Fork 54
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
plotting surfaces in jupyter notebook tutorial broken #177
Comments
TO DO -- use nilearn's plot_surf: |
I tried nilearn's plot_surf (https://nilearn.github.io/modules/generated/nilearn.plotting.plot_surf.html#nilearn.plotting.plot_surf) on mindboggle data:
but got the following error:
|
That might be a |
pinging @binarybottle to ask about current status: should I try to implement a corresponding fix? |
@PeerHerholz - that would be great. perhaps a quick look to see if niwidgets can be used may also be helpful. |
quick update re nilearn: there will be a fix in the next release of nilearn and nistats as mentioned by this neurostars post. As the problem is not related to nilearn but matplotlib (starting at version 3.1) we could either install nilearn from source or downgrade the matplotlib version. Otherwise, we would've to wait for the next release which should happen soon. Let me know what you think (I would vote for waiting for the next release). Re niwidgets: currently checking it. |
Wow, nice workaround, @PeerHerholz! |
@binarybottle should we go with the |
Sounds good!
Cheers,
@rno
Arno Klein, PhD
MATTER Lab Director
Joseph Healey Scholar
Senior Research Scientist
Child Mind Institute
101 E 56 St, NY, NY
matter.childmind.org
347-577-2091
…________________________________
From: Peer Herholz <[email protected]>
Sent: Tuesday, November 5, 2019 9:45:26 AM
To: nipy/mindboggle <[email protected]>
Cc: Arno Klein <[email protected]>; Mention <[email protected]>
Subject: Re: [nipy/mindboggle] plotting surfaces in jupyter notebook tutorial broken (#177)
@binarybottle<https://github.com/binarybottle> should we go with the nilearn version first, till I figure out the niwidgets part completely?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<#177?email_source=notifications&email_token=AABZX5EWEIVIWEJIIKU4YKLQSGBINA5CNFSM4HWTAJMKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEDC52YI#issuecomment-549838177>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AABZX5F6E7ELK5OHIBGIH7TQSGBINANCNFSM4HWTAJMA>.
|
@PeerHerholz - while nilearn can plot surfaces, i'm not sure it can plot the shape features. hence it may limit what you can do. in addition to niwidgets, you may want to take a look at vtk.js, which i know has been used in jupyter notebooks. |
@satra, yes. That's related to the examples and question I posted a bit further up. The example is based on depth values and the plotting seems to work (higher depth values further inside the cortex). The point I raised back then was how to tweak the plot to make it clearer and more interpretable. Was this your point? That although plots might work, they are not very comprehensive? In general, I like the I'll check out vtk.js. There's also itkwidgets, but going from |
The text was updated successfully, but these errors were encountered: