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annot.outline as a background #28
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Hi Andrew, thanks for the report and the great reproducible example. I can confirm that this seems to be a bug and I am looking into it. On the question regarding semi-transparent overlays: I also thought of that and it would be great to have that. I can't remember right now what exactly was the issue with that, but last time I started working on it it turned out to be a major pain, but I think it can be done. I think that rgl does not accept an alpha channel in colors at all, all you can do is set the transparency of the material. But I could implement the layer merging in a way that would still allow layers with alpha values, only in the end there would need to be a fixed (non-alpha) background color onto which all layers must be merged, resulting in a final non-alpha color passed to rgl. btw: I am working on something that should speed up the mesh neighborhood computation required to compute the outlines, it's too slow atm. |
Amazing, thanks!
From my position of near total ignorance about the inner workings of rgl... that would certainly seem to fit OK for the vis functions that have a
Great, it is a bit slow! For this purpose (common space = fsaverage) I have pre-computed it once and saved to the project directory. Thanks for providing this package to all - it's really useful! |
See also bug #14, I think this is related. |
I am trying to combine annot.outline (as a background) with a glm result as an overlay (specifically a cluster-masked sig).
annot.outline
looks great on its own, but when used as a background invis.symmetric.data.on.subject
the outlines appear monochrome black. I don't hate this, but it would be good to have the colour.Apologies if I've misread/misunderstood the docs or missed a known bug that explains this.
Bonus Question: is there a way to make the overlays in
vis[.symmetric].data.on.subject
semi-transparent? E.g. an alpha argument akin to desaturate? I guess this is not that easy with rgl, but I didn't see it in the faqs.Thanks in advance,
Andrew
The expected background:
![cm1](https://user-images.githubusercontent.com/4668209/125824337-16b20413-2131-44df-8032-c0a779b30099.png)
The result I get with
![cm2](https://user-images.githubusercontent.com/4668209/125824342-73c096f1-9ac0-4e16-ada5-e1cc673049d8.png)
vis.symmetric.data.on.subject
Environment:
Windows 10
R 4.0.3
fslbrain 0.5.0 (from github)
Script
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