Vessel segmentation and centerline extraction using 3D Slicer and VMTK

Demonstration of how 3D Slicer's Segment Editor module can be used for segmenting vessel tree and VMTK extension can extract and quantify centerline. Since the video was created additional features were added, such as computation of average radius, length, curvature, etc. of each branch.
3D Slicer and VMTK are completely free, open-source tools.
More information:
- VMTK extension: github.com/vmtk/SlicerExtensi...
- 3D Slicer: www.slicer.org
Any questions? Write to the 3D Slicer forum: discourse.slicer.org

[@hherhold]

Quick addition to the video text - on MacOS, it is Command-left click to add the region to the segment.

[@r4dl]

Hi. First of all, thank you for the great video! Im currently trying to segment the Aorta for a uni project: However, I can't manage such smooth results using this method? May I ask if there is any post-processing on the dataset before the segmentation shown in this video? Also, is this example publicly available?

[@AndrasLasso]

The image was not preprocessed in any way. All the steps are shown in the video, including downloading of the publicly available sample data set. If your image is lower quality then you can use smoothing effect in Segment Editor. If you have further questions, please post it to Slicer forum at discourse.slicer.org

[@faithshakoor8276]

Hello. Thank you for this demonstration. I'm experiencing some troubles when it comes to accessing the Effects handle once I've added a segment. Is there some type of extension that I need to access, or could it be my version? (I have version 5.2.2)

[@adamhendry945]

On an imported stl, I cannot create fiducials for centerline extraction

[@115p3r]

Does this approach work on MRI time-of-flight images? I tried to use the local threshold approach as in the video, but it won't create a 3D reconstruction. Is this only for CT images?

[@AndrasLasso]

It is not limited to specific imaging modality, so it should work on MRI ToF as well. We can help you further if you post your question on the Slicer forum (discourse.slicer.org).

[@115p3r]

@@AndrasLasso Thanks for the prompt response. I've posted in more detail on the site.

[@CP-ig3rg]

Hi, this is a great help for me. But I have a problem, that is, there is no "centerline conputation" in Vascular Modeling Toolkit modular, although I have install SilcerVMTK. Please help me, thank you.

[@PerkLabResearch]

Please write this question to the Slicer forum (discourse.slicer.org). Report you operating system and Slicer version.

[@gabrielbernardo5098]

My version is the 4.11 but, I dont have those effects like "Local Threshold" "FastMarching". Didn't find any option to add them. DO you know how ? Great tutorial, thank you !

[@AndrasLasso]

These additional Segment Editor effects are provided by SegmentEditorExtraEffects extension that you can install by a few clicks in the Extensions Manager.

[@gabrielbernardo5098]

@@AndrasLasso Will do it, thank you !!

[@gabrielbernardo5098]

@@AndrasLasso Thank you Andreas, it went well, but, I also have a doubt, if you can help me. I tried to find a tutorial but didn't find. I need a resource that hollow out the object (Like in solidworks the "shell" resource). The situation is, I need to 3D print an aorta but it has to be "hollow", I mean 2mm wall for example. Its to essay a surgery before go to the patient. Thank you !

[@AndrasLasso]

@@gabrielbernardo5098 You can use Hollow effect to make the object hollow and cut off end caps using Scissors. Please ask further questions on discourse.slicer.org.

[@al8fre7do]

Is is posibble to export the curve as .igs/.iges or .csv?

[@AndrasLasso]

You can get the curve point coordinates as a numpy array (using `arrayFromModelPoints`) and save them in any format you prefer. You can also do all the processing in Slicer in Python, combine the centerline with CAD models, create meshes, do quantifications, etc., so you might not even need to export the centerline.

[@mikolajbuchwald]

Is there a version of this video where the usage of "Extract Centerline" is presented, instead of "Centerline Computation"? The newer version of the plugin ("Extract Centerline") has way more options, and I was unable to extract centerlines with it. Maybe if I had a step-by-step video tutorial such as this one, I'd do better.

[@AndrasLasso]

Yes, this is a video showing Extract Centerline module: kzbin.info/www/bejne/r5qTaKCgp5h9m7c

[@mikolajbuchwald]

@@AndrasLasso , thank you! I will give it a try. Gosh, I see that I even commented the video you linked 7 months ago, but I was paying attention to some other aspect of the video back then.

[@mikolajbuchwald]

Works great. I think I didn't create a new Centerline curve before, and that's why it didn't work. Thanks for the help.

[@Mahalakshmi-xi8rm]

After centerline extraction how can i create a virtual navigation using endoscopy option where iam working on bronchoal tree

[@AndrasLasso]

You can use Endoscopy module

[@k.sankarkandasamy8152]

Is it possible to export this artery as step format

[@AndrasLasso]

STEP format is a CAD format. CAD software cannot deal with complex meshes coming from image segmentation (it may contain millions of points, while CAD software can typically deal with up to a couple of thousands).

[@k.sankarkandasamy8152]

Thanks for your reply dear. I want to import this segmented part into ansys or comsol for fluid flow analysis. So in which format should i export into.?

[@ReasatNabil]

Where I can get the data for this tutorial

[@AndrasLasso]

You can get the image from Sample Data module of 3D Slicer

[@ReasatNabil]

@@AndrasLasso thank you for your help