integrate fsleyes to generate rendered images for defacing module

[raamana]

fsleyes render --scene 3d -rot 45 0 -30 --outfile tmp.99.result.deface.fsleyes.render_1.png tmp.99.result.deface.nii -dr 30 250 -cr 30 500 -in spline -bf 0.225 -r 100 -ns 500

thanks to Arshitha and Eric from NIH

[raamana]

Hi @Arshitha, great meeting you in person at OHBM :). did you get a chance to work on this yet? Happy to do another zoom chat or code-review your progress so far. Let me know.

[Arshitha]

Hi @raamana - same, it was really nice to meet you in-person! I worked on it a bit during the conference but nothing substantial yet. I've carved out some time this Friday to pick up where I left off. I'll take up on your offer for a zoom call if I get stuck.

[raamana]

great, looking fwd to see this done :)

[Arshitha]

@raamana Hello again! I spent some time on the codebase today and added the 3D renders function and modified the CLI. I have not tested it yet but I'm fairly certain it won't work as it stands. Can we schedule a meeting for next meet so I can show you what i've done so far and also, ask questions? I can send you an email to setup a meeting.

If you'd like to check out the changes I've made, they're here https://github.com/Arshitha/visualqc/tree/cli-and-3d-renders

[raamana]

great to hear the progress, Arshitha! happy to meet later this week, but I'd suggest you give it a try to test, and see what errors you run into (beyond the basics of syntax and stringing the right functions together). That way, we can fix the issues. Its fine if you can't string them yet for lack of clarity or other issues, just let me know what they are.

I'm available in the evenings of Tuesday or thursday.

[raamana]

I'd start with testing the generate_3d_renders function directly first (and skip the whole visualqc entry points and lot of other validation) before writing tests for how it can be integrated.

if you already tested generate_3d_renders function directly on different renders, let me know.

FYI: A friend also sent us another way to generate renders btw, and we can keep that as another option in the future, depending on how easy or hard fsleyes proves to be across platforms and software versions etc
https://cerebro-viewer.readthedocs.io/en/latest/auto_examples/volume_surface_rendering/plot_volumetric_mask_as_surface.html#sphx-glr-auto-examples-volume-surface-rendering-plot-volumetric-mask-as-surface-py

[Arshitha]

I've tested generate_3d_renders function separately but I'll try testing it within vqcdeface tomorrow. Tuesday evenings work for me. I'll email to schedule something, and I'll also take a look at the cerebro-viewer link. Thanks!

[raamana]

Sounds good Arshitha :)