Operating system: macOS
Slicer version: 4.5
Good day all,
I am trying to create a 3D reconstruction of the portal vein and related structures. I have a CT with liver portal phase.
The radiology department at my institution tell me it’s not possible as the contrast intensity in a portal phase isn’t enough to differentiate from the surrounding tissue. My thinking is that it should be possible, as I can clearly see the portal structures by scrolling through the scan in the usual way.
I’ve tried using the rendering presets in Slicer but havent had much luck. Can anyone suggest another method? Or extension that specifically deals with this?
It should be doable. You can use the Segment Editor module to semi-automatically segment the vein.
Threshold effect can probably get you some of the larger vessels segments.
For segmenting smaller vessels you can:
Crop volume module to resample your input volume:
- set isotropic voxel spacing
- adjust Spacing scale to make the cropped volume spacing (shown in Volume information section) at least a few times smaller than the smallest vessel diameter that you want to segment
- adjust the region of interest to the minimum to keep the cropped image dimensions reasonable (preferably not more than a few hundred along each axis)
- Preprocess the image using
Vesselness filtering module in VMTK extension, which removes structures that has similar intensity as vessels but not have a tubular shape
Segment editor module, choose vesselness image as master volume and use Threshold effect and/or use Paint effect with intensity threshold to segment vessels.
Thanks Andras! I’ll give that a try…
I’m having some trouble following your advice. When I select the vessel
ness option under the VMTK module, I get and "error to load VMTK libraries
Why Slicer version do you use? What operating system?
Please try with the latest nightly version.
I don’t know if the method you mentioned can divide the femoral vein from the CT data.