AI-assisted segmentation using free tools - 3D Slicer and Nvidia Clara

This video shows how to do AI-assisted segmentation of tumors and organs on CT and MRI images using Nvidia Clara in 3D Slicer. The software is free, open-source, available on all desktop platforms. Please post any questions to 3D Slicer forum: discourse.slic...

[@gregortidholm]

This is very useful! Thank you for sharing!

[@Selmaelgrini]

Please, is there any extension for automatic segmentation in 3D Slicer

[@Muzahem96]

Annotation ct liver is not showing , is there a solution?

[@CraigDaly]

That looks fantastic. Thanks.

[@mikolajbuchwald]

Very impressive!

[@radyolojigrubu6256]

I want to use these segmentatitons to calculate some texture parameters. How can I do it? Is it only the 2D/3D presentations?

[@AndrasLasso]

You can segment some regions using Segment Editor module and then compute texture features in each region using SlicerRadiomics extension.

[@tylerchan5251]

6 sides boundary points are marked, press Start, Sent. --> Status: 500; Response: 500 Internal Server Error.

[@PerkLabResearch]

The demo server needs an upgrade. If this model keeps failing then you need to set up your own server or wait for the demo server"s upgrade (bu twe don't know when it will happen).

[@thalialeytonreto3498]

@@PerkLabResearch I just just got the same error! How can we set up our own server?

[@PerkLabResearch]

@@thalialeytonreto3498 See instructions here: github.com/NVIDIA/ai-assisted-annotation-client/tree/master/slicer-plugin#setup

[@kenny_tukin]

Do the user has to send the images to the NVIDIA server for the segmentation or the AI-segmentation tool is running completely in the local PC?

[@AndrasLasso]

It is up to you. You can either set up your own AIAA server (on your computer or anywhere else locally or remotely) or use Slicer's default server, which is currently hosted at Queen's University in Canada.

[@davidsibrina598]

@@AndrasLasso Can you please give me more information on where to connect to the Slicer default server. I would love to try this out. Thank you

[@AndrasLasso]

@@davidsibrina598 As described in the documentation (github.com/NVIDIA/ai-assisted-annotation-client/tree/master/slicer-plugin#nvidia-ai-assisted-annotation-aiaa-for-3d-slicer) leave the server field empty to use the default server.

[@user46346bdtgry]

where can i get more pre-trained ai models for ct (healthy) organ segmentation?

[@PerkLabResearch]

You can download models from NVidia NGC and there are various other model zoos (check out monai.io).

[@brad8122]

​@@PerkLabResearch Can we do this segmentation for a CT scan without any injected contrast, ? yours look like it has injected contrast for those organs?

[@PerkLabResearch]

@@brad8122 Certain structures and pathologies are only visible when contrast is used. Whatever is visible, you can train a model to recognize it. There have been a lot of progress in the field since the video was created. I would recommend to check out TotalSegmentator (100+ structures segmented in 2 minutes from any CT - see discourse.slicer.org/t/26710) and MONAILabel (for training your own model - see docs.monai.io/projects/label/en/latest/quickstart.html)

[@brad8122]

@@PerkLabResearch Thank you very very much but It raised lots of questions for me.
I am seeing lots of wavy structures on a kidney surface, also lots of spikes?
drive.google.com/file/d/1lcXFsDPfkMfdMLbz4-fylDFITw2lalTG/view?usp=share_link
i.imgur.com/Eg6kwzp.png
Why can it not show urinary tract canals/ureters for example? Can I train (or maybe just with a simple setting change) it to show those little details too?

[@AndrasLasso]

@@brad8122 There is no such thing as a perfect segmentation - it has to be just good enough for the specific clinical purpose. If you find that an AI model is not accurate enough for your application then you can add more and/or more accurate training data and and train more. Since all TotalSegmentator data sets are openly available, you can improve them and contribute back your changes and the maintainers can incorporate those in the next release.

[@arazmed]

İ get server error. How can i solve this

[@PerkLabResearch]

We switched to TotalSegmentator - github.com/wasserth/TotalSegmentator - for CT segmentation, which segments 100+ structures in 2 minutes, even without GPU; and MONAILabel - github.com/Project-MONAI/MONAILabel/tree/main/plugins/slicer#readme - that allows you to train your own models.

[@arazmed]

@@PerkLabResearch thank you

[@JOc17KER]

so the nvdia AIAA cannot be use anymore?@@PerkLabResearch

[@wanderingamerica5719]

@@PerkLabResearch do you have any tutorial for it?

[@aakib_parray1470]

It shows server error how to resolve it