Vessel segmentation on version 5.8.1 for mac

Support
1

Hi,

I am new to 3D slicer and am trying to segment the abdominal aorta for a study.

I have installed the SegmentEditorExtraEffects and SlicerVMTK extensions, and have been following the instructions found in this youtube video (https://www.youtube.com/watch?v=hm2x5Osn5GE) to try generate a 3D model of the segmented aorta.

However, when I try to use the Local Threshold effect, the CT images start flashing slowly (fade bright to dark in a slow strobing effect - making it difficult to assess the anatomy well) and when I try to generate the 3D image (by pressing command + left click over the segment of aorta I have selected with the yellow line) the 3D image generated is the entire abdomen - not the isolated aorta.

I tried installing the latest version of 3D slicer (5.8.1) and this did not fix the problem.
I have also tried using the 3D ‘centre view’ function and this did not help.

Help would be very much appreciated!

2

Assuming you are using a good quality CT scan with contrast intensity range between 300 and 500 in the big arteries, you may use the ‘Flood filling’ effect with a tolerance value between 70 and 110 and a ‘Neighbourhood size’ between 1.5 and 2.5 or more. It usually results in a fast and extended lumen segmentation.

You may also consider the “Quick artery segmentation” module in the SlicerVMTK extension. It proceeds as above and can do a little more in an automated way. 2 or 3 points, a box and off you go.