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rbumm / SlicerLungCTAnalyzer

This is a 3D Slicer extension for segmentation and spatial reconstruction of infiltrated, collapsed, and emphysematous areas in lung CT.
Apache License 2.0
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"Show output segments in 3D" takes very long #16

Closed rbumm closed 3 years ago

rbumm commented 3 years ago

... during the first run.

lassoan commented 3 years ago

It is due to having tens of millions of tiny surface segments because of the noisy voxel values and small details in the image. Probably the time could be reduced by 1-2 magnitudes if we apply smoothing (it consolidates few-voxel fragments into larger blobs). If you don't want to smooth then you can use volume rendering to visualize the results, similarly to the preview. You can adjust gradient opacity transfer function or maximum opacity projection mode, or set ventilated regions opacity to very low to ensure make dense regions show up well, from any viewpoint.

What is the goal of the 3D visualization? What do you need to see?

rbumm commented 3 years ago

Thanks for the explanation, I recently calculated the number of voxels myself and the numbers get breathtakingly high even in such a "small" 512 x 512 x 512 resolution.

What is the goal of the 3D visualization? What do you need to see?

The leading feature in Lung Analyzer should be reliable volume calculation for individual compartments. The 3D effect is a bit of overkill right now if all segments are displayed together, maybe it already helps if one reduces the number of visual segments. We see a lot of dorsal lung infiltrations in severe ARDS or COVID cases and our ICU doctors turn ventilated patients (prone) to counteract hydrostatic effects. 3D may help to better visualize the fluid-filled areas and demonstrate treatment effects. I will experiment on that display a bit and discuss it with the team ...

lassoan commented 3 years ago

We can have a quick interactive session with screen sharing so that I can show you what options are available. Give me a few timeslots that would work for you this week.

rbumm commented 3 years ago

That would great, I would be available best tomorrow, Tuesday 15th (15:00-20:00 UTC) or Friday 18th (13:00-16:00 UTC) ...

lassoan commented 3 years ago

Today (Tuesday) we give presentations at the Slicer project week, so unfortunately I'm not available, but Friday 15:00 UTC works well.

rbumm commented 3 years ago

Ok, confirmed ! Zoom ? Glad if you could DM me the details. I was not aware of the project week, very interesting, tried to register right now and hope to get a Zoom link.