Hello,
I’m working on a Moya Moya patient dataset, that includes T1w with Gadolinuim, CT, and arteriography.
I registered the images and segmented the skull, from the CT and also from the T1Gado using mri_synthstrip.
Now, I want to segment vessels, both on the arteriography and on the T1Gado.
Especially the ones close to or crossing the skull.
I started playing with various modules, but mostly used Volume Rendering to get that kind of image:
Both datasets look really nice. Did you try registering them? And did the vessels align well? The volume renderings look cluttered by noise (and enhancement from small vessels). Maybe try adding the two scans together with Add ScalarVolumes and then volume rendering or thresholding the result. This could cancel out the noise.
Dear Steve, thanks for your comment. I registered everything indeed. I’ll try following your advice. Sara also remembered me to look at related topics I’ll do that . Best
Hi Eric,
I am relatively new to 3D slicer and was wondering if you could instruct me on how to create a similar segmentation of the vessels. The data I am working with is a high resolution CT scan of mouse liver–I am interested in the connectivity of the vasculature.
Hi Anita,
Actually, I didn’t segment the vessels, I only loaded the arteriography (DCT) volume in the Volume Rendering plugin, chose a PreSet and play with the Shift value and Advanced …
My problem is indeed also to get a segmentation of the vessels.
I can share my data, and/or you can share yours, and I’ll try to play with it.
Let me know.
Best,
Eric
Hello again,
I played more with my data, and discussed more with my neurovascular neurosurgeon colleague.
Therefore, I can be more specific: I would like to segment the vasculature from the arterio image (DCT), but distinguish the carotid tree and tne meningeal tree.
I tried to use various modules to segment vessels, playing with Segment Editor tools, but failed.
Any hints / links / howto’s welcome!
I can share the volume I’m dealing with, too.
Images below illsutrate my attempts and show also, using volume rendering, the vasculature (both the carotid tree and the meningeal tree).
Thanks!
Eric
Maybe it worth to take a look at these recipes from András Lasso.
The one with segmentation by subtraction worked out pretty nice in our case. We segmented the syphon part of the carotid and had pretty nice results. True, it was more specific, and in general a smaller volume of interest, but still may worth a try.
Also the VMTK extension may worth another shot, even though it has its learning curve for sure
I’ll do that . Best
