# Vessel segmentation on version 5.8.1 for mac

**URL:** <https://discourse.slicer.org/t/vessel-segmentation-on-version-5-8-1-for-mac/42293>\
**Category:** Support\
**Created:** [March 25, 2025, 12:40pm UTC](https://discourse.slicer.org/t/vessel-segmentation-on-version-5-8-1-for-mac/42293 "2025-03-25T12:40:56Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![AlexM](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@AlexM](https://discourse.slicer.org/u/AlexM)\
**Post date:** [March 25, 2025, 12:40pm UTC](https://discourse.slicer.org/t/vessel-segmentation-on-version-5-8-1-for-mac/42293/1 "2025-03-25T12:40:56Z")

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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](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!

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<div class="post-metadata">

**Author:** ![chir.set](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/chir.set/32/66982_2.png) [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Post date:** [March 25, 2025, 2:00pm UTC](https://discourse.slicer.org/t/vessel-segmentation-on-version-5-8-1-for-mac/42293/2 "2025-03-25T14:00:14Z")

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> [@AlexM](#):
>
> for a study.

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.