Can we build some advanced tools for automatic pipline like mimics?

[lassoan (Andras Lasso)]

@xiang_luo

When i using Slicer, i want segment the lung lobe as accurate as mimics, i have paint it in CT slice bu slice

Have you tried LungCTAnalyzer extension?
It would be probably easy to come up with a semiautomatic solution for splitting the lung to lobes using classic methods, based on manually placed landmark points, curves, or planes, but nowadays this would only be used for generating training data for neural networks, so it is hard to justify the investment.

@xiang_luo

Automated advanced segment: It make new-users quick start with slicer to complete their work without have to be familiar with all basic tool in segmentation editor.

This is already available in NVidia AIAA segment editor effect. If we get more models, we can make more of them publicly available. Medical image computing researchers and NVidia are pushing MONAI very much (as a backend of NVidia Clara), so I would expect that we’ll have lots of models available in the coming years. It is hard to predict if researchers will make available their models freely or it will be all commercial.

@xiang_luo

Render more fast: When i use Mimics, i find it render so fast for any segmentation binary label map, while in Slicer, i find it’s more slow when i check the surfacing smooth. And the interacion in Mimics is more smooth.

Slicer is a much more generic tool, with much more features than Mimics, which makes it harder to match the performance, but we try to address all pain points. For example, Segment smoothing has been 20x faster (thanks to Kitware investing into improving the corresponding filter in VTK) in recent Slicer Preview releases, so the overhead of surface smoothing is now negligible. There are also experiments for using direct volume rendering for 3D display of segmentations, but since 3D update typically takes less than a second now and can be easily enabled/disabled, this is not on the critical path anymore. If you have performance issues when trying to accomplish a specific workflow then let us know.

@xiang_luo

Some morphology operation: i find the grow/shrink in margin in segment editor not action as what i expected. I think there shoud be some morphology like dilation/erode in the segmentation for only process the 8/26-connected component for N iteration in pixel level. In Slicer, i find the processing always in size level, like 3mm, 1mm.

In Slicer all display, processing, parametrization are in physical space, in 3D. This way, you can run the same visualization, processing, quantification workflow on a wide variety of inputs without major changes in the parameters. For example, you want to fill holes that are “less than 1mm”, and not that are “less than 3 voxels”, because 1mm makes sense clinically, but 3 voxels only makes sense for a particular image, along a particular volume axis.