# Segmenting vasculature on MRI scans (non MRA)

**URL:** <https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498>\
**Category:** Support\
**Created:** [July 22, 2024, 1:59pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498 "2024-07-22T13:59:07Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![BDhoth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bdhoth/32/78752_2.png) [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Post date:** [July 22, 2024, 1:59pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498/1 "2024-07-22T13:59:07Z")

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What is the best way to segment out vasculature on MRI scans? Normally a post T1 is provided.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 22, 2024, 9:36pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498/2 "2024-07-22T21:36:03Z")

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Which vessels? How well they are visible? Can you post a few images?

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**Author:** ![BDhoth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bdhoth/32/78752_2.png) [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Post date:** [July 23, 2024, 4:57pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498/3 "2024-07-23T16:57:05Z")

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![Screenshot 2024-07-22 215145](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/a/4acbc56997356fcb87a5acfe9d7f3663e9038432.jpeg)  
It is very case dependent. Thus far I have just been thresholding and highlighting the areas of concern.  
Thank you for your help.

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**Author:** ![tsinesh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tsinesh/32/16670_2.png) [@tsinesh](https://discourse.slicer.org/u/tsinesh)\
**Post date:** [July 25, 2024, 12:14pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498/4 "2024-07-25T12:14:02Z")

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Hello Becky,

You are interested in cerebral venes, right?

Try local threshold (you have to install extra modul called SlicerSegmentEditorExtraEffects.)

My tutorial (to get some ideas) how to segment cerebral arteries you can find here. [Extracting STL from DICOM images to generate Brain Arteries geometry - #6 by tsinesh](https://discourse.slicer.org/t/extracting-stl-from-dicom-images-to-generate-brain-arteries-geometry/25215/6)

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**Author:** ![BDhoth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bdhoth/32/78752_2.png) [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Post date:** [July 31, 2024, 12:54pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498/5 "2024-07-31T12:54:32Z")

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Thank you for this. I attempted the vesselness filter as I think that would be best for what I need, but maybe the extensions has changed slightly? There were multiple options and none with the “seed point” option.

 ![Screenshot 2024-07-31 075148](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/7/f72b458349bab227a97f393e560d37c13ff6fab6.png)

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**Author:** ![tsinesh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tsinesh/32/16670_2.png) [@tsinesh](https://discourse.slicer.org/u/tsinesh)\
**Post date:** [July 31, 2024, 2:49pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-on-mri-scans-non-mra/37498/6 "2024-07-31T14:49:26Z")

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Yes, your modul look different. I hadfor arteries good experiences with frangi filter.